Fc VARIANTS WITH ALTERED BINDING TO FcRn

ABSTRACT

The present application relates to optimized IgG immunoglobulin variants, engineering methods for their generation, and their application, particularly for therapeutic purposes.

This application is a continuation of U.S. patent application Ser. No.15/709,334, filed Sep. 19, 2017, which is a divisional of U.S. patentapplication Ser. No. 14/318,001, filed Jun. 27, 2014, now abandoned,which is a continuation of U.S. patent application Ser. No. 11/932,151,filed Oct. 31, 2007, now U.S. Pat. No. 8,802,820 which claims benefitunder 35 U.S.C. § 119(e) to U.S. Ser. No. 60/951,536 filed Jul. 24,2007, both entirely incorporated by reference.

The instant application contains a Sequence Listing which has beensubmitted electronically in ASCII format and is hereby incorporated byreference in its entirety. Said ASCII copy, created on Aug. 4, 2020, isnamed 067461-5026-US29_Sequence_Listing_ST25.txt and is 59,371 bytes insize.

FIELD OF THE INVENTION

The present application relates to optimized IgG immunoglobulinvariants, engineering methods for their generation, and theirapplication, particularly for therapeutic purposes.

BACKGROUND OF THE INVENTION

Antibodies are immunological proteins that bind a specific antigen. Inmost mammals, including humans and mice, antibodies are constructed frompaired heavy and light polypeptide chains. Each chain is made up ofindividual immunoglobulin (Ig) domains, and thus the generic termimmunoglobulin is used for such proteins. Each chain is made up of twodistinct regions, referred to as the variable and constant regions. Thelight and heavy chain variable regions show significant sequencediversity between antibodies, and are responsible for binding the targetantigen. The constant regions show less sequence diversity, and areresponsible for binding a number of natural proteins to elicit importantbiochemical events. In humans there are five different classes ofantibodies including IgA (which includes subclasses IgA1 and IgA2), IgD,IgE, IgG (which includes subclasses IgG1, IgG2, IgG3, and IgG4), andIgM. The distinguishing feature between these antibody classes is theirconstant regions, although subtler differences may exist in the Vregion. FIG. 1 shows an IgG1 antibody, used here as an example todescribe the general structural features of immunoglobulins. IgGantibodies are tetrameric proteins composed of two heavy chains and twolight chains. The IgG heavy chain is composed of four immunoglobulindomains linked from N- to C-terminus in the order VH-CH1-CH2-CH3,referring to the heavy chain variable domain, heavy chain constantdomain 1, heavy chain constant domain 2, and heavy chain constant domain3 respectively (also referred to as VH-Cγ1-Cγ2-Cγ3, referring to theheavy chain variable domain, constant gamma 1 domain, constant gamma 2domain, and constant gamma 3 domain respectively). The IgG light chainis composed of two immunoglobulin domains linked from N- to C-terminusin the order VL-CL, referring to the light chain variable domain and thelight chain constant domain respectively.

The variable region of an antibody contains the antigen bindingdeterminants of the molecule, and thus determines the specificity of anantibody for its target antigen. The variable region is so named becauseit is the most distinct in sequence from other antibodies within thesame class. The majority of sequence variability occurs in thecomplementarity determining regions (CDRs). There are 6 CDRs total,three each per heavy and light chain, designated VH CDR1, VH CDR2, VHCDR3, VL CDR1, VL CDR2, and VL CDR3. The variable region outside of theCDRs is referred to as the framework (FR) region. Although not asdiverse as the CDRs, sequence variability does occur in the FR regionbetween different antibodies. Overall, this characteristic architectureof antibodies provides a stable scaffold (the FR region) upon whichsubstantial antigen binding diversity (the CDRs) can be explored by theimmune system to obtain specificity for a broad array of antigens. Anumber of high-resolution structures are available for a variety ofvariable region fragments from different organisms, some unbound andsome in complex with antigen. The sequence and structural features ofantibody variable regions are well characterized (Morea et al., 1997,Biophys Chem 68:9-16; Morea et al., 2000, Methods 20:267-279, entirelyincorporated by reference), and the conserved features of antibodieshave enabled the development of a wealth of antibody engineeringtechniques (Maynard et al., 2000, Annu Rev Biomed Eng 2:339-376,entirely incorporated by reference). For example, it is possible tograft the CDRs from one antibody, for example a murine antibody, ontothe framework region of another antibody, for example a human antibody.This process, referred to in the art as “humanization”, enablesgeneration of less immunogenic antibody therapeutics from nonhumanantibodies. Fragments including the variable region can exist in theabsence of other regions of the antibody, including for example theantigen binding fragment (Fab) including VH-Cγ1 and VH-CL, the variablefragment (Fv) including VH and VL, the single chain variable fragment(scFv) including VH and VL linked together in the same chain, as well asa variety of other variable region fragments (Little et al., 2000,Immunol Today 21:364-370, entirely incorporated by reference).

The Fc region of an antibody interacts with a number of Fc receptors andligands, imparting an array of important functional capabilitiesreferred to as effector functions. For IgG the Fc region, as shown inFIGS. 1 and 2, comprises Ig domains Cγ2 and Cγ3 and the N-terminal hingeleading into Cγ2. An important family of Fc receptors for the IgG classis the Fc gamma receptors (FcγRs). These receptors mediate communicationbetween antibodies and the cellular arm of the immune system (Raghavanet al., 1996, Annu Rev Cell Dev Biol 12:181-220; Ravetch et al., 2001,Annu Rev Immunol 19:275-290, both entirely incorporated by reference).In humans this protein family includes FcγRI (CD64), including isoformsFcγRIa, FcγRIb, and FcγRIc; FcγRII (CD32), including isoforms FcγRIIa(including allotypes H131 and R131), FcγRIIb (including FcγRIIb-1 andFcγRIIb-2), and FcγRIIc; and FcγRIII (CD16), including isoforms FcγRIIIa(including allotypes V158 and F158) and FcγRIIIb (including allotypesFcγRIIIb-NA1 and FcγRIIIb-NA2) (Jefferis et al., 2002, Immunol Lett82:57-65, entirely incorporated by reference). These receptors typicallyhave an extracellular domain that mediates binding to Fc, a membranespanning region, and an intracellular domain that may mediate somesignaling event within the cell. These receptors are expressed in avariety of immune cells including monocytes, macrophages, neutrophils,dendritic cells, eosinophils, mast cells, platelets, B cells, largegranular lymphocytes, Langerhans' cells, natural killer (NK) cells, andγγ T cells. Formation of the Fc/FcγR complex recruits these effectorcells to sites of bound antigen, typically resulting in signaling eventswithin the cells and important subsequent immune responses such asrelease of inflammation mediators, B cell activation, endocytosis,phagocytosis, and cytotoxic attack. The ability to mediate cytotoxic andphagocytic effector functions is a potential mechanism by whichantibodies destroy targeted cells. The cell-mediated reaction whereinnonspecific cytotoxic cells that express FcγRs recognize bound antibodyon a target cell and subsequently cause lysis of the target cell isreferred to as antibody dependent cell-mediated cytotoxicity (ADCC)(Raghavan et al., 1996, Annu Rev Cell Dev Biol 12:181-220; Ghetie etal., 2000, Annu Rev Immunol 18:739-766; Ravetch et al., 2001, Annu RevImmunol 19:275-290, all entirely incorporated by reference). Thecell-mediated reaction wherein nonspecific cytotoxic cells that expressFcγRs recognize bound antibody on a target cell and subsequently causephagocytosis of the target cell is referred to as antibody dependentcell-mediated phagocytosis (ADCP). A number of structures have beensolved of the extracellular domains of human FcγRs, including FcγRIIa(pdb accession code 1 H9V, entirely incorporated byreference)(Sondermann et al., 2001, J Mol Biol 309:737-749, entirelyincorporated by reference) (pdb accession code 1FCG, entirelyincorporated by reference)(Maxwell et al., 1999, Nat Struct Biol6:437-442, entirely incorporated by reference), FcγRIIb (pdb accessioncode 2FCB, entirely incorporated by reference)(Sondermann et al., 1999,Embo J 18:1095-1103, entirely incorporated by reference); and FcγRIIIb(pdb accession code 1 E4J, entirely incorporated byreference)(Sondermann et al., 2000, Nature 406:267-273, entirelyincorporated by reference.). All FcγRs bind the same region on Fc, atthe N-terminal end of the Cγ2 domain and the preceding hinge, shown inFIG. 1. This interaction is well characterized structurally (Sondermannet al., 2001, J Mol Biol 309:737-749, entirely incorporated byreference), and several structures of the human Fc bound to theextracellular domain of human FcγRIIIb have been solved (pdb accessioncode 1 E4K, entirely incorporated by reference)(Sondermann et al., 2000,Nature 406:267-273, entirely incorporated by reference) (pdb accessioncodes 1 IIS and 1 IIX, entirely incorporated by reference)(Radaev etal., 2001, J Biol Chem 276:16469-16477, entirely incorporated byreference), as well as has the structure of the human IgE Fc/FcεRIαcomplex (pdb accession code 1F6A, entirely incorporated byreference)(Garman et al., 2000, Nature 406:259-266, entirelyincorporated by reference). The effector function response may bemodified by variant in the Fc region (Lazar et al. 2006 Proc. Nat. Acad.Sci USA. 103(111):4005-4010, entirely incorporated by reference).

The different IgG subclasses have different affinities for the FcγRs,with IgG1 and IgG3 typically binding substantially better to thereceptors than IgG2 and IgG4 (Jefferis et al., 2002, Immunol Lett82:57-65, entirely incorporated by reference). All FcγRs bind the sameregion on IgG Fc, yet with different affinities: the high affinitybinder FcγRI has a Kd for IgG1 of 10⁻⁸ M⁻¹, whereas the low affinityreceptors FcγRII and FcγRII generally bind at 10⁻⁶ and 10⁻⁵respectively. The extracellular domains of FcγRIIIa and FcγRIIIb are 96%identical; however FcγRIIIb does not have an intracellular signalingdomain. Furthermore, whereas FcγRI, FcγRIIa/c, and FcγRIIIa are positiveregulators of immune complex-triggered activation, characterized byhaving an intracellular domain that has an immunoreceptor tyrosine-basedactivation motif (ITAM), FcγRIIb has an immunoreceptor tyrosine-basedinhibition motif (ITIM) and is therefore inhibitory. Thus the former arereferred to as activation receptors, and FcγRIIb is referred to as aninhibitory receptor. The receptors also differ in expression pattern andlevels on different immune cells. Yet another level of complexity is theexistence of a number of FcγR polymorphisms in the human proteome. Aparticularly relevant polymorphism with clinical significance isV158/F158 FcγRIIIa. Human IgG1 binds with greater affinity to the V158allotype than to the F158 allotype. This difference in affinity, andpresumably its effect on ADCC and/or ADCP, has been shown to be asignificant determinant of the efficacy of the anti-CD20 antibodyrituximab (Rituxan®, Biogenldec). Patients with the V158 allotyperespond favorably to rituximab treatment; however, patients with thelower affinity F158 allotype respond poorly (Cartron et al., 2002, Blood99:754-758, entirely incorporated by reference). Approximately 10-20% ofhumans are V158/V158 homozygous, 45% are V158/F158 heterozygous, and35-45% of humans are F158/F158 homozygous (Lehrnbecher et al., 1999,Blood 94:4220-4232; Cartron et al., 2002, Blood 99:754-758, all entirelyincorporated by reference). Thus 80-90% of humans are poor responders,i.e., they have at least one allele of the F158 FcγRIIIa.

An overlapping but separate site on Fc, shown in FIG. 1, serves as theinterface for the complement protein C1q. In the same way that Fc/FcγRbinding mediates ADCC, Fc/C1q binding mediates complement dependentcytotoxicity (CDC). C1q forms a complex with the serine proteases C1rand C1s to form the C1 complex. C1q is capable of binding sixantibodies, although binding to two IgGs is sufficient to activate thecomplement cascade. Similar to Fc interaction with FcγRs, different IgGsubclasses have different affinity for C1q, with IgG1 and IgG3 typicallybinding substantially better to the FcγRs than IgG2 and IgG4 (Jefferiset al., 2002, Immunol Lett 82:57-65, entirely incorporated byreference).

In IgG, a site on Fc between the Cg2 and Cg3 domains (FIG. 1) mediatesinteraction with the neonatal receptor FcRn, the binding of whichrecycles endocytosed antibody from the endosome back to the bloodstream(Raghavan et al., 1996, Annu Rev Cell Dev Biol 12:181-220; Ghetie etal., 2000, Annu Rev Immunol 18:739-766, both entirely incorporated byreference). This process, coupled with preclusion of kidney filtrationdue to the large size of the full-length molecule, results in favorableantibody serum half-lives ranging from one to three weeks. Binding of Fcto FcRn also plays a key role in antibody transport. The binding site onFc for FcRn is also the site at which the bacterial proteins A and Gbind. The tight binding by these proteins is typically exploited as ameans to purify antibodies by employing protein A or protein G affinitychromatography during protein purification. Thus the fidelity of thisregion on Fc is important for both the clinical properties of antibodiesand their purification. Available structures of the rat Fc/FcRn complex(Burmeister et al., 1994, Nature, 372:379-383; Martin et al., 2001, MolCell 7:867-877, both entirely incorporated by reference), and of thecomplexes of Fc with proteins A and G (Deisenhofer, 1981, Biochemistry20:2361-2370; Sauer-Eriksson et al., 1995, Structure 3:265-278; Tashiroet al., 1995, Curr Opin Struct Biol 5:471-481, all entirely incorporatedby reference), provide insight into the interaction of Fc with theseproteins. The FcRn receptor is also responsible for the transfer of IgGto the neo-natal gut and to the lumen of the intestinal epithelia inadults (Ghetie and Ward, Annu. Rev. Immunol., 2000, 18:739-766; Yoshidaet al., Immunity, 2004, 20(6):769-783, both entirely incorporated byreference).

Studies of rat and human Fc domains have demonstrated the importance ofsome Fc residues to the binding of FcRn. The rat and human sequenceshave about 64% sequence identity in the Fc regions (residues 237-443 inthe numbering of Kabat et al.). See FIGS. 3, 4, and 5 for the rat/humanalignments of Fc, FcRn heavy chain, and FcRn light chain(beta-2-microglobulin). A model of the human Fc/FcRn complex has beenbuilt from the existing structure of the rat Fc/FcRn complex (Martin etal., 2001, Mol Cell 7:867-877, entirely incorporated by reference). Therat and human sequences share some residues that are critical for FcRnbinding, such as H310 and H435 (Medesan et al., 1997 J. Immunol.158(5):221-7; Shields et al., 2001, J. Biol. Chem. 276(9):6591-6604,both entirely incorporated by reference). In many positions, however,the human and rat proteins have different amino acids, giving theresidues in the human sequence different environments, and possibly adifferent identities, than in the rat sequence. This variability limitsthe ability to transfer characteristics from one homolog to the otherhomolog.

In the murine Fc, random mutation and phage display selection at thesites, T252, T254, and T256 lead to a triple mutant, T252L/T254S/T256F,that has a 3.5-fold increase in FcRn affinity and a 1.5-fold increase inserum half-life (Ghetie et al., 1997, Nat. Biotech. 15(7): 637-640,entirely incorporated by reference). Disruption of the Fc/FcRninteraction by mutations at positions 253, 310 and 435 also lead todecreased in vivo half-life (Medesan et al J. Immunol. 1997158(5):2211-7, entirely incorporated by reference).

The crystal structures of the rat Fc/FcRn complex identified importantFc residues for FcRn binding (Burmeister et al. Nature. 372:379-383(1994); Martin et al. Molecular Cell. 7:867-877 (2001), both entirelyincorporated by reference). The original Fc/FcRn complex structure wassolved in 1994 to a resolution of 6 Å (Table 2a, Burmeister et al.Nature. 372:379-383 (1994), entirely incorporated by reference). Thehigher resolution structure, solved in 2001 by Mann et al, showed a moredetailed view of the side chains positions (Martin et al. MolecularCell. 7:867-877 (2001), entirely incorporated by reference). Thiscrystal structure of rat Fc bound to rat FcRn was solved using an Fcdimer with one monomer containing the mutationsT252G/I253G/T254G/H310E/H433E/H435E, which disrupt FcRn binding, and onemonomer containing a wild-type Fc monomer.

Mutational studies in human Fcγ have been done on some of the residuesthat are important for binding to FcRn and have demonstrated anincreased serum half-life. In human Fcγ1, Hinton et al. mutated threeresidues individually to the other 19 common amino acids. Hinton et al.,found that some point mutants a double mutant increased the FcRn bindingaffinity (Hinton et al., 2004, J. Biol. Chem. 279(8): 6213-6216. Hintonet al. Journal of Immunology 2006, 176:346-356, both entirelyincorporated by reference). Two mutations had increased half-lives inmonkeys. Shields et al. mutated residues, almost exclusively to Ala, andstudied their binding to FcRn and the FcγR's (Shields et al., 2001, J.Biol. Chem., 276(9):6591-6604, entirely incorporated by reference).

Dall'Acqua et al. used phage display to select for Fc mutations thatbound FcRn with increased affinity (Dall'Acqua et al. 2002, J. Immunol.169:5171-5180, entirely incorporated by reference). The DNA sequencesselected for were primarily double and triple mutants. The referenceexpressed the proteins encoded by many of their selected sequences andfound some that bound to FcRn more tightly than the wild-type Fc.

The administration of antibodies and Fc fusion proteins as therapeuticsrequires injections with a prescribed frequency relating to theclearance and half-life characteristics of the protein. Longer in vivohalf-lives allow more seldom injections or lower dosing, which isclearly advantageous. Although the past mutations in the Fc domain havelead to some proteins with increased FcRn binding affinity and in vivohalf-lives, these mutations have not identified the optimal mutationsand enhanced in vivo half-life.

One feature of the Fc region is the conserved N-linked glycosylationthat occurs at N297, shown in FIG. 1. This carbohydrate, oroligosaccharide as it is sometimes referred, plays a critical structuraland functional role for the antibody, and is one of the principlereasons that antibodies must be produced using mammalian expressionsystems. Umana et al., 1999, Nat Biotechnol 17:176-180; Davies et al.,2001, Biotechnol Bioeng 74:288-294; Mimura et al., 2001, J Biol Chem276:45539-45547.; Radaev et al., 2001, J Biol Chem 276:16478-16483;Shields et al., 2001, J Biol Chem 276:6591-6604; Shields et al., 2002, JBiol Chem 277:26733-26740; Simmons et al., 2002, J Immunol Methods263:133-147; Radaev et al., 2001, J Biol Chem 276:16469-16477; and Krappet al., 2003, J Mol Biol 325:979-989, all entirely incorporated byreference).

Antibodies have been developed for therapeutic use. Representativepublications related to such therapies include Chamow et al., 1996,Trends Biotechnol 14:52-60; Ashkenazi et al., 1997, Curr Opin Immunol9:195-200, Cragg et al., 1999, Curr Opin Immunol 11:541-547; Glennie etal., 2000, Immunol Today 21:403-410, McLaughlin et al., 1998, J ClinOncol 16:2825-2833, and Cobleigh et al., 1999, J Clin Oncol17:2639-2648, all entirely incorporated by reference. Currently foranticancer therapy, any small improvement in mortality rate definessuccess. Certain IgG variants disclosed herein enhance the capacity ofantibodies to limit further growth or destroy at least partially,targeted cancer cells.

Anti-tumor potency of antibodies is via enhancement of their ability tomediate cytotoxic effector functions such as ADCC, ADCP, and CDC.Examples include Clynes et al., 1998, Proc Natl Acad Sci USA 95:652-656;Clynes et al., 2000, Nat Med 6:443-446 and Carton et al., 2002, Blood99:754-758, both entirely incorporated by reference.

Human IgG1 is the most commonly used antibody for therapeutic purposes,and the majority of engineering studies have been constructed in thiscontext. The different isotypes of the IgG class however, includingIgG1, IgG2, IgG3, and IgG4, have unique physical, biological, andclinical properties. There is a need in the art to design improved IgG1,IgG2, IgG3, and IgG4 variants. There is a further need to design suchvariants to improve binding to FcRn and/or increase in vivo half-life ascompared to native IgG polypeptides. Additionally, there is a need tocombine variants with improved pharmacokinetic properties with variantscomprising modifications to improve efficacy through altered FcgammaRbinding. The present application meets these and other needs.

SUMMARY OF THE INVENTION

The present application is directed to Fc variants of a parentpolypeptide including at least one modification in the Fc region of thepolypeptide. In various embodiments, the variant polypeptides exhibitaltered binding to FcRn as compared to a parent polypeptide. In certainvariations, the modification can be selected from the group consistingof: 246H, 246S, 247D, 247T, 248H, 248P, 248Q, 248R, 248Y, 249T, 249W,250E, 250I, 250Q, 250V, 251D, 251E, 251H, 251I, 251K, 251M, 251N, 251T,251V, 251Y, 252Q, 252Y, 253L, 253T, 253V, 254H, 254L, 254N, 254T, 254V,A254N, 255E, 255F, 255H, 255K, 255S, 255V, 256E, 256V, 257A, 257C, 257D,257E, 257F, 257G, 257H, 257I, 257K, 257L, 257M, 257N, 257Q, 257R, 257S,257T, 257V, 257W, 257Y, 258R, 258V, 259I, 279A, 279D, 279C, 279F, 279G,279H, 279I, 279K, 279M, 279N, 279P, 279Q, 279Q, 279R, 279S, 279T, 279W,279Y, 280H, {circumflex over ( )}281A, {circumflex over ( )}281 D,{circumflex over ( )}281S, {circumflex over ( )}281I, 282D, 282F, 282H,282I, 282T, 283F, 283I, 283L, 283Y, 284H, 284K, 284P, 284Q, 284R, 284S,284Y, 285S, 285V, 286D, 286#, 286L, 287H, 287S, 287V, 287Y, 288H, 288Q,288S, 305H, 305T, 306F, 306H, 306I, 306N, 306T, 306V, 306Y, 307D, 307P,307Q, 307S, 307V, 307Y, 308C, 308D, 308E, 308F, 308G, 308H, 308I, 308K,308L, 308M, 308N, 308Q, 308P, 308R, 308S, 308W, 308Y, 309F, 309H, 309N,309Q, 309V, 309Y, 310K, 310N, 310T, 311A, 311L, 311P, 311T, 311V, 311W,312H, 313Y, 315E, 315G, 315H, 315Q, 315S, 315T, 317H, 317S, 319F, 319F,319L, 339P, 340P, 341S, 374H, 374S, 376H, 376L, 378H, 378N, 380A, 380T,380Y, 382H, 383H, 383K, 383Q, 384E, 384G, 384H, 385A, 385C, 385F, 385H,385I, 385K, 385L, 385M, 385N, 385P, 385Q, 385S, 385T, 385V, 385W, 385Y,386E, 386K, 387#, 387A, 387H, 387K, 387Q, 389E, 389H, 426E, 426H, 426L,426N, 426R, 426V, 426Y, 427I, 428F, 428L, 429D, 429F, 429K, 429N, 429Q,429S, 429T, 429Y, 430D, 430H, 430K, 430L, 430Q, 430Y, 431G, 431H, 431I,431P, 431P, 431S, 432F, 432H, 432N, 432S, 432V, 433E, 433P, 433S, 434A,434F, 434H, 434L, 434M, 434Q, 434S, 434Y, 435N, 436E, 436F, 436L, 436V,436W, 437E, 437V, 438H, and 438K, where the numbering is according tothe EU Index in Kabat et al. and {circumflex over ( )} is an insertionafter the identified position and # is a deletion of the identifiedposition.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 250Q/252Y, 250Q/256E, 250Q/286D,250Q/308F, 250Q/308Y, 250Q/311A, 250Q/311V, 250Q/380A, 250Q/428L,250Q/428F, 250Q/434H, 250Q/434F, 250Q/434Y, 250Q/434A, 250Q/434M, and250Q/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 250E/252Y, 250E/256E, 250E/286D,250E/308F, 250E/308Y, 250E/311A, 250E/311V, 250E/380A, 250E/428L,250E/428F, 250E/434H, 250E/434F, 250E/434Y, 250E/434A, 250E/434M, and250E/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 252Y/250Q, 252Y/250E, 252Y/256E,252Y/286D, 252Y/308F, 252Y/308Y, 252Y/311A, 252Y/311V, 252Y/380A,252Y/428L, 252Y/428F, 252Y/434H, 252Y/434F, 252Y/434Y, 252Y/434A,252Y/434M, and 252Y/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 256E/250Q, 256E/250E, 256E/252Y,256E/286D, 256E/308F, 256E/308Y, 256E/311A, 256E/311V, 256E/380A,256E/428L, 256E/428F, 256E/434H, 256E/434F, 256E/434Y, 256E/434A,256E/434M, and 256E/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 286D/250Q, 286D/250E, 286D/252Y,286D/256E, 286D/308F, 286D/308Y, 286D/311A, 286D/311V, 286D/380A,286D/428L, 286D/428F, 286D/434H, 286D/434F, 286D/434Y, 286D/434A,286D/434M, and 286D/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 308F/250Q, 308F/250E, 308F/252Y,308F/256E, 308F/286D, 308F/311A, 308F/311V, 308F/380A, 308F/428L,308F/428F, 308F/434H, 308F/434F, 308F/434Y, 308F/434A, 308F/434M, and308F/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 308Y/250Q, 308Y/250E, 308Y/252Y,308Y/256E, 308Y/286D, 308Y/311A, 308Y/311V, 308Y/380A, 308Y/428L,308Y/428F, 308Y/434H, 308Y/434F, 308Y/434Y, 308Y/434A, 308Y/434M, and308Y/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 311A/250Q, 311A/250E, 311A/252Y,311A/256E, 311A/286D, 311A/308F, 311A/308Y, 311A/380A, 311A/428L,311A/428F, 311A/434H, 311A/434F, 311A/434Y, 311A/434A, 311A/434M, and311A/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 311V/250Q, 311V/250E, 311V/252Y,311V/256E, 311V/286D, 311V/308F, 311V/308Y, 311V/380A, 311V/428L,311V/428F, 311V/434H, 311V/434F, 311V/434Y, 311V/434A, 311V/434M, and311V/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 380A/250Q, 380A/250E, 380A/252Y,380A/256E, 380A/286D, 380A/308F, 380A/308Y, 380A/311A, 380A/311V,380A/428L, 380A/428F, 380A/434H, 380A/434F, 380A/434Y, 380A/434A,380A/434M, and 380A/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 428L/250Q, 428L/250E, 428L/252Y,428L/256E, 428L/286D, 428L/308F, 428L/308Y, 428L/311A, 428L/311V,428L/380A, 428L/434H, 428L/434F, 428L/434Y, 428L/434A, 428L/434M, and428L/434S.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434H/250Q, 434H/250E, 434H/252Y,434H/256E, 434H/286D, 434H/308F, 434H/308Y, 434H/311A, 434H/311V,434H/380A, 434H/428L, and 434H/428F.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434F/250Q, 434F/250E, 434F/252Y,434F/256E, 434F/286D, 434F/308F, 434F/308Y, 434F/311A, 434F/311V,434F/380A, 434F/428L, and 434F/428F.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434Y/250Q, 434Y/250E, 434Y/252Y,434Y/256E, 434Y/286D, 434Y/308F, 434Y/308Y, 434Y/311A, 434Y/311V,434Y/380A, 434Y/428L, and 434Y/428F.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434A/250Q, 434A/250E, 434A/252Y,434A/256E, 434A/286D, 434A/308F, 434A/308Y, 434A/311A, 434A/311V,434A/380A, 434A/428L, and 434A/428F.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434M/250Q, 434M/250E, 434M/252Y,434M/256E, 434M/286D, 434M/308F, 434M/308Y, 434M/311A, 434M/311V,434M/380A, 434M/428L, and 434M/428F.

In another variation, the Fc variant includes at least two modificationsselected from the group consisting of: 434S/250Q, 434S/250E, 434S/252Y,434S/256E, 434S/286D, 434S/308F, 434S/308Y, 434S/311A, 434S/311V,434S/380A, 434S/428L, and 434S/428F.

In another variation, the Fc variant includes at least one modificationselected from the group consisting of: Y319L, T307Q, V259I, M252Y,V259I/N434S, M428L/N434S, V308F/N434S, M252Y/S254T/T256E/N434S,M252Y/S254T/T256E/V308F, M252Y/S254T/T256E/M428L, V308F/M428L/N434S,V259I/V308F/N434S, T307QN308F/N434S, T250I/V308F/N434S,V308F/Y319L/N434S, V259I/V308F/M428L, V259I/T307Q/V308F,T250I/V259I/V308F, V259I/V308F/Y319L, T307Q/V308F/L309Y,T307Q/V308F/Y319L, and T250Q/V308F/M428L.

In another variation, the Fc variant includes at least one modificationselected from the group consisting of: Y319L, T307Q, V259I, M252Y,V259I/N434S, M428L/N434S, V308F/N434S, V308F/M428L/N434S,V259I/V308F/N434S, T307Q/V308F/N434S, T250I/V308F/N434S,V308F/Y319L/N434S, V259I/V308F/M428L, V259I/T307Q/V308F,T250I/V2591/V308F, V259I/V308F/Y319L, T307Q/V308F/L309Y,T307Q/V308F/Y319L, and T250Q/V308F/M428L.

In another variation, the Fc variant includes at least one modificationselected from the group consisting of: 250I, 250V, 252Q, 252Y, 254T,256V, 259I, 307P, 307Q, 307S, 308F, 309N, 309Y, 311P, 319F, 319L, 428L,and 434S.

In another variation, the Fc variant includes at least one modificationselected from the group consisting of: 250V/308F, 250I/308F, 254T/308F,256V/308F, 259I/308F, 307P/208F, 307Q/308F, 307S/308F, 308F/309Y,308F/309Y, V308F/311P, 308F/319L, 308F/319F, 308F/428L, 252Q/308F,M252Y/S254T/T256E, 259I/434S, 428L/434S, 308F/434S, 308F/428L/434S,259I/308F/434S, 307Q/308F/434S, 250I/308F/434S, 308F/319L/434S,259I/308F/428L, 259I/307Q/308F, 250I/259I/308F, 259I/308F/319L,307Q/308F/309Y, 307Q/308F/319L, and 250Q/308F/428L.

In another variation, the invention includes a method of treating apatient in need of said treatment comprising administering an effectiveamount of an Fc variant described herein.

In another variation, the invention includes a method of increasing thehalf-life of an antibody or immunoadhesin by modifying an Fc accordingto the modifications described herein.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Antibody structure and function. Shown is a model of a fulllength human IgG1 antibody, modeled using a humanized Fab structure frompdb accession code 1CE1 (James et al., 1999, J Mol Biol 289:293-301,entirely incorporated by reference) and a human IgG1 Fc structure frompdb accession code 1DN2 (DeLano et al., 2000, Science 287:1279-1283,entirely incorporated by reference). The flexible hinge that links theFab and Fc regions is not shown. IgG1 is a homodimer of heterodimers,made up of two light chains and two heavy chains. The Ig domains thatcomprise the antibody are labeled, and include V_(L) and C_(L)for thelight chain, and V_(H), Cgamma1 (Cγ1), Cgamma2 (Cγ2), and Cgamma3 (Cγ3)for the heavy chain. The Fc region is labeled. Binding sites forrelevant proteins are labeled, including the antigen binding site in thevariable region, and the binding sites for FcγRs, FcRn, C1q, andproteins A and G in the Fc region.

FIG. 2. Human IgG sequences used in the present invention with the EUnumbering as in Kabat et al.

FIG. 3. Example human and rodent IgG sequences used in the presentinvention with the EU numbering as in Kabat.

FIG. 4. Example human and rodent FcRn heavy chain sequences used in thepresent invention.

FIG. 5. Example human and rodent beta-2-microglobulin sequences used inthe present invention.

FIG. 6. A human Fc/FcRn complex model created from the rat structures(Burmeister et al., 1994, Nature, 372:379-383; Martin et al., 2001, MolCell 7:867-877, both entirely incorporated by reference). Some histidineresidues are shown in space-filling atoms on the FcRn chains (lightgrey) and Fc polypeptide (dark grey).

FIG. 7. IIlustration of some concepts used in the design of variantscomprising insertions or deletions.

FIG. 8a -8 b. Variants of the present invention.

FIG. 9a -9 b. Variants of the present invention.

FIG. 10a -10 b. Variants of the present invention.

FIG. 11. Diagram of the vector pcDNA3.1 Zeo+, which may be used in theconstruct of Fc variants.

FIG. 12a -12 b. Competition FcRn binding data of wild-type Fc and Fcvariants of the present invention. In each panel, the Fc variants of thepresent invention are shown as the left (red or dark grey) curve and thewild-type anti-HER2 antibody is shown as the right (blue or light grey)curve.

FIGS. 13a -13 j. Summary of FcRn binding properties of the Fc variants.The columns from left to right show the FcRn binding modifications, theimmunoglobulin used, other modifications, the relative FcRn affinity byAlphaScreen™ competition assays compared to wild type (median value),and the number of assays performed. Relative FcRn affinity numbersgreater than 1.0 demonstrate increased binding over wild type. Data werecollected at pH 6.0 (0.1M sodium phosphate, 25 mM sodium chloride).

FIG. 14a -14 d. FcRn binding data of Fc variants. The Fc variants are inalemtuzumab or anti-HER2 antibody. Shown are the fold-increases inbinding compared to wild type, that is, numbers greater than oneindicate tighter binding to FcRn whereas numbers less than one indicatereduced binding to FcRn.

FIG. 15. Summary of surface plasmon resonance experiments of Fc variantswith improved binding to FcRn. The bar graph shows the fold-increase inFcRn binding affinity of each variant relative to wild-type Fc domain.

FIG. 16a -16 b. Surface plasmon resonance experiments of wild-typeantibody and variants of the present invention. The traces shown are theassociation and dissociation of the Fc variant antibody to FcRn atpH6.0.

FIG. 17a -17 c. Binding assays of Fc variants of the present inventionto FcRn. Shown are direct binding assays measured by AlphaScreen™ at pH6.0 (a and b) and pH 7.0 (c).

FIG. 18. Binding assays of Fc variants of the present invention to FcRn.Shown are the surface plasmon resonance units created upon binding ofthe variant Fc to surface-bound FcRn.

FIG. 19. Surface plasmon resonance measurement of the binding affinityof Fc variants of the present invention to human FcRn at pH 6.0.

FIG. 20. Summary of surface plasmon resonance (SPR) measurements of thebinding affinity of Fc variants of the present invention with human,macaque and mouse FcRn. Numbers greater than one indicate increasedbinding of the variant Fc to FcRn as determined by fitting SPR curves toa 1:1 Langmuir binding model.

FIG. 21a -21 b. Summary of FcRn binding properties of the Fc variants.The columns from left to right show the FcRn binding modifications, theimmunoglobulin used, other modifications, the relative FcRn affinity byAlphaScreen™ competition assays compared to wild type (median value),and the number of assays performed. Relative FcRn affinity numbersgreater than 1.0 demonstrate increased binding over wild type. Data werecollected at pH 6.0 (0.1M sodium phosphate, 125mM sodium chloride).

FIG. 22. Amino acid sequences of the anti-HER2 antibody heavy and lightchains.

FIG. 23. Amino acid sequences of the constant regions (CH1 to CH3) ofthe some IgG1 heavy chains used herein.

FIG. 24. Amino acid sequences of the constant regions (CH1 to CH3) ofthe some hybrid IgG1/2 heavy chains used herein.

FIG. 25. Fc variants binding to the human FcgammaRIIIA (V158 Allotype)as determined with AlphaScreen™ competition assays.

FIG. 26. Fc variants binding binding to protein A as determined withAlphaScreen™ competition assays.

FIG. 27. Serum concentrations of WT and variants of antibodies in humanFcRn knockin mice. Anti-VEGF antibodies used were the WT (open squares),V308F (closed squares), P257L (closed triagles) and P257N (crosses).

FIG. 28. Examples of FcRn binding variants of the present invention.Anti-VEGF antibodies are listed with the volume of culture media and theyield of purified protein.

FIG. 29. Binding affinity of variants of the present invention to humanFcRn at pH6.0. The values shown are fold increase in binding strength ofthe variant in question to the wild-type antibody. For example, thevariant 434S binds to FcRn 4.4-fold more tightly than does the wild-typeantibody.

FIG. 30. Binding of WT and variant antibodies to FcRn on the surface of293T cells.

FIG. 31a -31 b. Combination variants of the present invention comprisingmultiple substitutions.

FIG. 32. A picture of the intereactions of a variant human CH3 domaincomprising 434S, labeled Ser434, and human FcRn.

DETAILED DESCRIPTION OF THE INVENTION

The present invention discloses the generation of novel variants of Fcdomains, including those found in antibodies, Fc fusions, andimmuno-adhesions, which have an increased binding to the FcRn receptor.As noted herein, binding to FcRn results in longer serum retention invivo.

In order to increase the retention of the Fc proteins in vivo, theincrease in binding affinity must be at around pH 6 while maintaininglower affinity at around pH 7.4. Although still under examination, Fcregions are believed to have longer half-lives in vivo, because bindingto FcRn at pH 6 in an endosome sequesters the Fc (Ghetie and Ward, 1997Immunol Today. 18(12): 592-598, entirely incorporated by reference). Theendosomal compartment then recycles the Fc to the cell surface. Once thecompartment opens to the extracellular space, the higher pH, ˜7.4,induces the release of Fc back into the blood. In mice, Dall'Acqua etal. showed that Fc mutants with increased FcRn binding at pH 6 and pH7.4 actually had reduced serum concentrations and the same half life aswild-type Fc (Dall' Acqua et al. 2002, J. Immunol. 169:5171-5180,entirely incorporated by reference). The increased affinity of Fc forFcRn at pH 7.4 is thought to forbid the release of the Fc back into theblood. Therefore, the Fc mutations that will increase Fc's half-life invivo will ideally increase FcRn binding at the lower pH while stillallowing release of Fc at higher pH. The amino acid histidine changesits charge state in the pH range of 6.0 to 7.4. Therefore, it is notsurprising to find His residues at important positions in the Fc/FcRncomplex (FIG. 6.)

An additional aspect of the invention is the increase in FcRn bindingover wild type specifically at lower pH, about pH 6.0, to facilitateFc/FcRn binding in the endosome. Also disclosed are Fc variants withaltered FcRn binding and altered binding to another class of Fcreceptors, the FcγR's (sometimes written FcgammaR's) as differentialbinding to FcγRs, particularly increased binding to FcγRIIIb anddecreased binding to FcγRIIb, has been shown to result in increasedefficacy.

Definitions

In order that the application may be more completely understood, severaldefinitions are set forth below. Such definitions are meant to encompassgrammatical equivalents.

By “ADCC” or “antibody dependent cell-mediated cytotoxicity” as usedherein is meant the cell-mediated reaction wherein nonspecific cytotoxiccells that express FcγRs recognize bound antibody on a target cell andsubsequently cause lysis of the target cell.

By “ADCP” or antibody dependent cell-mediated phagocytosis as usedherein is meant the cell-mediated reaction wherein nonspecific cytotoxiccells that express FcγRs recognize bound antibody on a target cell andsubsequently cause phagocytosis of the target cell.

By “modification” herein is meant an amino acid substitution, insertion,and/or deletion in a polypeptide sequence or an alteration to a moietychemically linked to a protein. For example, a modification may be analtered carbohydrate or PEG structure attached to a protein. By “aminoacid modification” herein is meant an amino acid substitution,insertion, and/or deletion in a polypeptide sequence.

By “amino acid substitution” or “substitution” herein is meant thereplacement of an amino acid at a particular position in a parentpolypeptide sequence with another amino acid. For example, thesubstitution E272Y refers to a variant polypeptide, in this case an Fcvariant, in which the glutamic acid at position 272 is replaced withtyrosine.

By “amino acid insertion” or “insertion” as used herein is meant theaddition of an amino acid sequence at a particular position in a parentpolypeptide sequence. For example, -233E or {circumflex over ( )}233Edesignates an insertion of glutamic acid after position 233 and beforeposition 234. Additionally, -233ADE or {circumflex over ( )}233ADEdesignates an insertion of AlaAspGlu after position 233 and beforeposition 234.

By “amino acid deletion” or “deletion” as used herein is meant theremoval of an amino acid sequence at a particular position in a parentpolypeptide sequence. For example, E233- or E233# designates a deletionof glutamic acid at position 233. Additionally, EDA233- or EDA233#designates a deletion of the sequence GluAspAla that begins at position233.

By “variant protein” or “protein variant”, or “variant” as used hereinis meant a protein that differs from that of a parent protein by virtueof at least one amino acid modification. Protein variant may refer tothe protein itself, a composition comprising the protein, or the aminosequence that encodes it. Preferably, the protein variant has at leastone amino acid modification compared to the parent protein, e.g. fromabout one to about ten amino acid modifications, and preferably fromabout one to about five amino acid modifications compared to the parent.The protein variant sequence herein will preferably possess at leastabout 80% homology with a parent protein sequence, and most preferablyat least about 90% homology, more preferably at least about 95%homology. Variant protein can refer to the variant protein itself,compositions comprising the protein variant, or the DNA sequence thatencodes it. Accordingly, by “antibody variant” or “variant antibody” asused herein is meant an antibody that differs from a parent antibody byvirtue of at least one amino acid modification, “IgG variant” or“variant IgG” as used herein is meant an antibody that differs from aparent IgG by virtue of at least one amino acid modification, and“immunoglobulin variant” or “variant immunoglobulin” as used herein ismeant an immunoglobulin sequence that differs from that of a parentimmunoglobulin sequence by virtue of at least one amino acidmodification. “Fc variant” or “variant Fc” as used herein is meant aprotein comprising a modification in an Fc domain. The Fc variants ofthe present invention are defined according to the amino acidmodifications that compose them. Thus, for example, I332E is an Fcvariant with the substitution I332E relative to the parent Fcpolypeptide. Likewise, S239D/I332E/G236A defines an Fc variant with thesubstitutions S239D, I332E, and G236A relative to the parent Fcpolypeptide. The identity of the WT amino acid may be unspecified, inwhich case the aforementioned variant is referred to as 239D/332E/236A.It is noted that the order in which substitutions are provided isarbitrary, that is to say that, for example, S239D/I332E/G236A is thesame Fc variant as G236A/S239D/I332E, and so on. For all positionsdiscussed in the present invention, numbering is according to the EUindex or EU numbering scheme (Kabat et al., 1991, Sequences of Proteinsof Immunological Interest, 5th Ed., United States Public Health Service,National Institutes of Health, Bethesda, hereby entirely incorporated byreference). The EU index or EU index as in Kabat or EU numbering schemerefers to the numbering of the EU antibody (Edelman et al., 1969, ProcNatl Acad Sci USA 63:78-85, hereby entirely incorporated by reference.)The modification can be an addition, deletion, or substitution.Substitutions can include naturally occurring amino acids andnon-naturally occurring amino acids. Variants may comprise non-naturalamino acids. Examples include U.S. Pat. No. 6,586,207; WO 98/48032; WO03/073238; US2004-0214988A1; WO 05/35727A2; WO 05/74524A2; J. W. Chin etal., (2002), Journal of the American Chemical Society 124:9026-9027; J.W. Chin, & P. G. Schultz, (2002), ChemBioChem 11:1135-1137; J. W. Chin,et al., (2002), PICAS United States of America 99:11020-11024; and, L.Wang, & P. G. Schultz, (2002), Chem. 1-10, all entirely incorporated byreference.

As used herein, “protein” herein is meant at least two covalentlyattached amino acids, which includes proteins, polypeptides,oligopeptides and peptides. The peptidyl group may comprise naturallyoccurring amino acids and peptide bonds, or synthetic peptidomimeticstructures, i.e. “analogs”, such as peptoids (see Simon et al., PNAS USA89(20):9367 (1992), entirely incorporated by reference). The amino acidsmay either be naturally occurring or non-naturally occurring; as will beappreciated by those in the art. For example, homo-phenylalanine,citrulline, and noreleucine are considered amino acids for the purposesof the invention, and both D- and L-(R or S) configured amino acids maybe utilized. The variants of the present invention may comprisemodifications that include the use of unnatural amino acids incorporatedusing, for example, the technologies developed by Schultz andcolleagues, including but not limited to methods described by Cropp &Shultz, 2004, Trends Genet. 20(12):625-30, Anderson et al., 2004, ProcNatl Acad Sci USA 101(2):7566-71, Zhang et al., 2003, 303(5656):371-3,and Chin et al., 2003, Science 301(5635):964-7, all entirelyincorporated by reference. In addition, polypeptides may includesynthetic derivatization of one or more side chains or termini,glycosylation, PEGylation, circular permutation, cyclization, linkers toother molecules, fusion to proteins or protein domains, and addition ofpeptide tags or labels.

By “residue” as used herein is meant a position in a protein and itsassociated amino acid identity. For example, Asparagine 297 (alsoreferred to as Asn297, also referred to as N297) is a residue in thehuman antibody IgG1.

By “Fab” or “Fab region” as used herein is meant the polypeptide thatcomprises the VH, CH1, VL, and CL immunoglobulin domains. Fab may referto this region in isolation, or this region in the context of a fulllength antibody, antibody fragment or Fab fusion protein.

By “IgG subclass modification” as used herein is meant an amino acidmodification that converts one amino acid of one IgG isotype to thecorresponding amino acid in a different, aligned IgG isotype. Forexample, because IgG1 comprises a tyrosine and IgG2 a phenylalanine atEU position 296, a F296Y substitution in IgG2 is considered an IgGsubclass modification.

By “non-naturally occurring modification” as used herein is meant anamino acid modification that is not isotypic. For example, because noneof the IgGs comprise a glutamic acid at position 332, the substitutionI332E in IgG1, IgG2, IgG3, or IgG4 is considered a non-naturallyoccuring modification.

By “amino acid” and “amino acid identity” as used herein is meant one ofthe 20 naturally occurring amino acids or any non-natural analogues thatmay be present at a specific, defined position.

By “effector function” as used herein is meant a biochemical event thatresults from the interaction of an antibody Fc region with an Fcreceptor or ligand. Effector functions include but are not limited toADCC, ADCP, and CDC.

By “effector cell” as used herein is meant a cell of the immune systemthat expresses one or more Fc receptors and mediates one or moreeffector functions. Effector cells include but are not limited tomonocytes, macrophages, neutrophils, dendritic cells, eosinophils, mastcells, platelets, B cells, large granular lymphocytes, Langerhans'cells, natural killer (NK) cells, and γδT cells, and may be from anyorganism including but not limited to humans, mice, rats, rabbits, andmonkeys.

By “IgG Fc ligand” as used herein is meant a molecule, preferably apolypeptide, from any organism that binds to the Fc region of an IgGantibody to form an Fc/Fc ligand complex. Fc ligands include but are notlimited to FcγRs, FcγRs, FcγRs, FcRn, C1q, C3, mannan binding lectin,mannose receptor, staphylococcal protein A, streptococcal protein G, andviral FcγR. Fc ligands also include Fc receptor homologs (FcRH), whichare a family of Fc receptors that are homologous to the FcγRs (Davis etal., 2002, Immunological Reviews 190:123-136, entirely incorporated byreference). Fc ligands may include undiscovered molecules that bind Fc.Particular IgG Fc ligands are FcRn and Fc gamma receptors. By “Fcligand” as used herein is meant a molecule, preferably a polypeptide,from any organism that binds to the Fc region of an antibody to form anFc/Fc ligand complex.

By “Fc gamma receptor”, “FcγR” or “FcgammaR” as used herein is meant anymember of the family of proteins that bind the IgG antibody Fc regionand is encoded by an FcγR gene. In humans this family includes but isnot limited to FcγRI (CD64), including isoforms FcγRIa, FcγRIb, andFcγRIc; FcγRII (CD32), including isoforms FcγRIIa (including allotypesH131 and R131), FcγRIIb (including FcγRIIb-1 and FcγRIIb-2), andFcγRIIc; and FcγRIII (CD16), including isoforms FcγRIIIa (includingallotypes V158 and F158) and FcγRIIIb (including allotypes FcγRIIIb-NA1and FcγRIIIb-NA2) (Jefferis et al., 2002, Immunol Lett 82:57-65,entirely incorporated by reference), as well as any undiscovered humanFcγRs or FcγR isoforms or allotypes. An FcγR may be from any organism,including but not limited to humans, mice, rats, rabbits, and monkeys.Mouse FcγRs include but are not limited to FcγRI (CD64), FcγRII (CD32),FcγRIII (CD16), and FcγRIII-2 (CD16-2), as well as any undiscoveredmouse FcγRs or FcγR isoforms or allotypes.

By “FcRn” or “neonatal Fc Receptor” as used herein is meant a proteinthat binds the IgG antibody Fc region and is encoded at least in part byan FcRn gene. The FcRn may be from any organism, including but notlimited to humans, mice, rats, rabbits, and monkeys. As is known in theart, the functional FcRn protein comprises two polypeptides, oftenreferred to as the heavy chain and light chain. The light chain isbeta-2-microglobulin and the heavy chain is encoded by the FcRn gene.Unless other wise noted herein, FcRn or an FcRn protein refers to thecomplex of FcRn heavy chain with beta-2-microglobulin. Sequences ofparticular interest of FcRn are shown in the Figures, particularly thehuman species.

By “parent polypeptide” as used herein is meant an unmodifiedpolypeptide that is subsequently modified to generate a variant. Theparent polypeptide may be a naturally occurring polypeptide, or avariant or engineered version of a naturally occurring polypeptide.Parent polypeptide may refer to the polypeptide itself, compositionsthat comprise the parent polypeptide, or the amino acid sequence thatencodes it. Accordingly, by “parent immunoglobulin” as used herein ismeant an unmodified immunoglobulin polypeptide that is modified togenerate a variant, and by “parent antibody” as used herein is meant anunmodified antibody that is modified to generate a variant antibody. Itshould be noted that “parent antibody” includes known commercial,recombinantly produced antibodies as outlined below.

By “position” as used herein is meant a location in the sequence of aprotein. Positions may be numbered sequentially, or according to anestablished format, for example the EU index as in Kabat. For example,position 297 is a position in the human antibody IgG1.

By “target antigen” as used herein is meant the molecule that is boundspecifically by the variable region of a given antibody. A targetantigen may be a protein, carbohydrate, lipid, or other chemicalcompound.

By “target cell” as used herein is meant a cell that expresses a targetantigen.

By “variable region” as used herein is meant the region of animmunoglobulin that comprises one or more Ig domains substantiallyencoded by any of the VΘ, Vλ, and/or VH genes that make up the kappa,lambda, and heavy chain immunoglobulin genetic loci respectively.

By “wild type or WT” herein is meant an amino acid sequence or anucleotide sequence that is found in nature, including allelicvariations. A WT protein has an amino acid sequence or a nucleotidesequence that has not been intentionally modified.

The present invention is directed to antibodies that exhibit moduluatedbinding to FcRn (modulation including increased as well as decreasedbinding). For example, in some instances, increased binding results incellular recycling of the antibody and hence increased half-life, forexample for therapeutic antibodies. Alternatively, decreased FcRnbinding is desirable, for example for diagnostic antibodies ortherapeutic antibodies that contain radiolabels. In addition, antibodiesexhibiting increased binding to FcRn and altered binding to other Fcreceptors, eg. FcγRs, find use in the present invention. Accordingly,the present invention provides antibodies.

Antibodies

The present application is directed to antibodies that include aminoacid modifications that modulate binding to FcRn. Of particular interestare antibodies that minimally comprise an Fc region, or functionalvariant thereof, that displays increased binding affinity to FcRn atlowered pH, and do not exhibit substantially altered binding at higherpH.

Traditional antibody structural units typically comprise a tetramer.Each tetramer is typically composed of two identical pairs ofpolypeptide chains, each pair having one “light” (typically having amolecular weight of about 25 kDa) and one “heavy” chain (typicallyhaving a molecular weight of about 50-70 kDa). Human light chains areclassified as kappa and lambda light chains. Heavy chains are classifiedas mu, delta, gamma, alpha, or epsilon, and define the antibody'sisotype as IgM, IgD, IgG, IgA, and IgE, respectively. IgG has severalsubclasses, including, but not limited to IgG1, IgG2, IgG3, and IgG4.IgM has subclasses, including, but not limited to, IgM1 and IgM2. Thus,“isotype” as used herein is meant any of the subclasses ofimmunoglobulins defined by the chemical and antigenic characteristics oftheir constant regions. The known human immunoglobulin isotypes areIgG1, IgG2, IgG3, IgG4, IgA1, IgA2, IgM1, IgM2, IgD, and IgE.

The amino-terminal portion of each chain includes a variable region ofabout 100 to 110 or more amino acids primarily responsible for antigenrecognition. In the variable region, three loops are gathered for eachof the V domains of the heavy chain and light chain to form anantigen-binding site. Each of the loops is referred to as acomplementarity-determining region (hereinafter referred to as a “CDR”),in which the variation in the amino acid sequence is most significant.

The carboxy-terminal portion of each chain defines a constant regionprimarily responsible for effector function. Kabat et al. collectednumerous primary sequences of the variable regions of heavy chains andlight chains. Based on the degree of conservation of the sequences, theyclassified individual primary sequences into the CDR and the frameworkand made a list thereof (see SEQUENCES OF IMMUNOLOGICAL INTEREST, 5thedition, NIH publication, No. 91-3242, E.A. Kabat et al., entirelyincorporated by reference).

In the IgG subclass of immunoglobulins, there are several immunoglobulindomains in the heavy chain. By “immunoglobulin (Iq) domain” herein ismeant a region of an immunoglobulin having a distinct tertiarystructure. Of interest in the present invention are the heavy chaindomains, including, the constant heavy (CH) domains and the hingedomains. In the context of IgG antibodies, the IgG isotypes each havethree CH regions. Accordingly, “CH” domains in the context of IgG are asfollows: “CH1” refers to positions 118-220 according to the EU index asin Kabat. “CH2” refers to positions 237-340 according to the EU index asin Kabat, and “CH3” refers to positions 341-447 according to the EUindex as in Kabat.

Another type of Ig domain of the heavy chain is the hinge region. By“hinge” or “hinge region” or “antibody hinge region” or “immunoglobulinhinge region” herein is meant the flexible polypeptide comprising theamino acids between the first and second constant domains of anantibody. Structurally, the IgG CH1 domain ends at EU position 220, andthe IgG CH2 domain begins at residue EU position 237. Thus for IgG theantibody hinge is herein defined to include positions 221 (D221 in IgG1)to 236 (G236 in IgG1), wherein the numbering is according to the EUindex as in Kabat. In some embodiments, for example in the context of anFc region, the lower hinge is included, with the “lower hinge” generallyreferring to positions 226 or 230.

Of particular interest in the present invention are the Fc regions. By“Fc” or “Fc region”, as used herein is meant the polypeptide comprisingthe constant region of an antibody excluding the first constant regionimmunoglobulin domain and in some cases, part of the hinge. Thus Fcrefers to the last two constant region immunoglobulin domains of IgA,IgD, and IgG, the last three constant region immunoglobulin domains ofIgE and IgM, and the flexible hinge N-terminal to these domains. For IgAand IgM, Fc may include the J chain. For IgG, as illustrated in FIG. 1,Fc comprises immunoglobulin domains Cgamma2 and Cgamma3 (Cg2 and Cg3)and the lower hinge region between Cgamma1 (Cg1) and Cgamma2 (Cg2).Although the boundaries of the Fc region may vary, the human IgG heavychain Fc region is usually defined to include residues C226 or P230 toits carboxyl-terminus, wherein the numbering is according to the EUindex as in Kabat. Fc may refer to this region in isolation, or thisregion in the context of an Fc polypeptide, as described below. By “Fcpolypeptide” as used herein is meant a polypeptide that comprises all orpart of an Fc region. Fc polypeptides include antibodies, Fc fusions,isolated Fcs, and Fc fragments.

In some embodiments, the antibodies are full length. By “full lengthantibody” herein is meant the structure that constitutes the naturalbiological form of an antibody, including variable and constant regions,including one or more modifications as outlined herein.

Alternatively, the antibodies can be a variety of structures, including,but not limited to, antibody fragments, monoclonal antibodies,bispecific antibodies, minibodies, domain antibodies, syntheticantibodies (sometimes referred to herein as “antibody mimetics”),chimeric antibodies, humanized antibodies, antibody fusions (sometimesreferred to as “antibody conjugates”), and fragments of each,respectively.

Antibody Fragments

In one embodiment, the antibody is an antibody fragment. Of particularinterest are antibodies that comprise Fc regions, Fc fusions, and theconstant region of the heavy chain (CH1-hinge-CH2-CH3), again alsoincluding constant heavy region fusions.

Specific antibody fragments include, but are not limited to, (i) the Fabfragment consisting of VL, VH, CL and CH1 domains, (ii) the Fd fragmentconsisting of the VH and CH1 domains, (iii) the Fv fragment consistingof the VL and VH domains of a single antibody; (iv) the dAb fragment(Ward et al., 1989, Nature 341:544-546, entirely incorporated byreference) which consists of a single variable, (v) isolated CDRregions, (vi) F(ab′)2 fragments, a bivalent fragment comprising twolinked Fab fragments (vii) single chain Fv molecules (scFv), wherein aVH domain and a VL domain are linked by a peptide linker which allowsthe two domains to associate to form an antigen binding site (Bird etal., 1988, Science 242:423-426, Huston et al., 1988, Proc. Natl. Acad.Sci. U.S.A. 85:5879-5883, entirely incorporated by reference), (viii)bispecific single chain Fv (WO 03/11161, hereby incorporated byreference) and (ix) “diabodies” or “triabodies”, multivalent ormultispecific fragments constructed by gene fusion (Tomlinson et. al.,2000, Methods Enzymol. 326:461-479; WO94/13804; Holliger et al., 1993,Proc. Natl. Acad. Sci. U.S.A. 90:6444-6448, all entirely incorporated byreference). The antibody fragments may be modified. For example, themolecules may be stabilized by the incorporation of disulphide bridgeslinking the VH and VL domains (Reiter et al., 1996, Nature Biotech.14:1239-1245, entirely incorporated by reference).

Chimeric and Humanized Antibodies

In some embodiments, the scaffold components can be a mixture fromdifferent species. As such, if the protein is an antibody, such antibodymay be a chimeric antibody and/or a humanized antibody. In general, both“chimeric antibodies” and “humanized antibodies” refer to antibodiesthat combine regions from more than one species. For example, “chimericantibodies” traditionally comprise variable region(s) from a mouse (orrat, in some cases) and the constant region(s) from a human. “Humanizedantibodies” generally refer to non-human antibodies that have had thevariable-domain framework regions swapped for sequences found in humanantibodies. Generally, in a humanized antibody, the entire antibody,except the CDRs, is encoded by a polynucleotide of human origin or isidentical to such an antibody except within its CDRs. The CDRs, some orall of which are encoded by nucleic acids originating in a non-humanorganism, are grafted into the beta-sheet framework of a human antibodyvariable region to create an antibody, the specificity of which isdetermined by the engrafted CDRs. The creation of such antibodies isdescribed in, e.g., WO 92/11018, Jones, 1986, Nature 321:522-525,Verhoeyen et al., 1988, Science 239:1534-1536, all entirely incorporatedby reference. “Backmutation” of selected acceptor framework residues tothe corresponding donor residues is often required to regain affinitythat is lost in the initial grafted construct (U.S. Pat. Nos. 5,530,101;5,585,089; 5,693,761; 5,693,762; 6,180,370; 5,859,205; 5,821,337;6,054,297; 6,407,213, all entirely incorporated by reference). Thehumanized antibody optimally also will comprise at least a portion of animmunoglobulin constant region, typically that of a humanimmunoglobulin, and thus will typically comprise a human Fc region.Humanized antibodies can also be generated using mice with a geneticallyengineered immune system. Roque et al., 2004, Biotechnol. Prog.20:639-654, entirely incorporated by reference. A variety of techniquesand methods for humanizing and reshaping non-human antibodies are wellknown in the art (See Tsurushita & Vasquez, 2004, Humanization ofMonoclonal Antibodies, Molecular Biology of B Cells, 533-545, ElsevierScience (USA), and references cited therein, all entirely incorporatedby reference). Humanization methods include but are not limited tomethods described in Jones et al., 1986, Nature 321:522-525; Riechmannet al., 1988; Nature 332:323-329; Verhoeyen et al., 1988, Science,239:1534-1536; Queen et al., 1989, Proc Natl Acad Sci, USA 86:10029-33;He et al., 1998, J. Immunol. 160: 1029-1035; Carter et al., 1992, ProcNatl Acad Sci USA 89:4285-9, Presta et al., 1997, Cancer Res.57(20):4593-9; Gorman et al., 1991, Proc. Natl. Acad. Sci. USA88:4181-4185; O'Connor et al., 1998, Protein Eng 11:321-8, all entirelyincorporated by reference. Humanization or other methods of reducing theimmunogenicity of nonhuman antibody variable regions may includeresurfacing methods, as described for example in Roguska et al., 1994,Proc. Natl. Acad. Sci. USA 91:969-973, entirely incorporated byreference. In one embodiment, the parent antibody has been affinitymatured, as is known in the art. Structure-based methods may be employedfor humanization and affinity maturation, for example as described inU.S. Ser. No. 11/004,590. Selection based methods may be employed tohumanize and/or affinity mature antibody variable regions, including butnot limited to methods described in Wu et al., 1999, J. Mol. Biol.294:151-162; Baca et al., 1997, J. Biol. Chem. 272(16):10678-10684;Rosok et al., 1996, J. Biol. Chem. 271(37): 22611-22618; Rader et al.,1998, Proc. Natl. Acad. Sci. USA 95: 8910-8915; Krauss et al., 2003,Protein Engineering 16(10):753-759, all entirely incorporated byreference. Other humanization methods may involve the grafting of onlyparts of the CDRs, including but not limited to methods described inU.S. Ser. No. 09/810,510; Tan et al., 2002, J. Immunol. 169:1119-1125;De Pascalis et al., 2002, J. Immunol. 169:3076-3084, all entirelyincorporated by reference.

Bispecific Antibodies

In one embodiment, the antibodies of the invention multispecificantibody, and notably a bispecific antibody, also sometimes referred toas “diabodies”. These are antibodies that bind to two (or more)different antigens. Diabodies can be manufactured in a variety of waysknown in the art (Holliger and Winter, 1993, Current Opinion Biotechnol.4:446-449, entirely incorporated by reference), e.g., preparedchemically or from hybrid hybridomas.

Minibodies

In one embodiment, the antibody is a minibody. Minibodies are minimizedantibody-like proteins comprising a scFv joined to a CH3 domain. Hu etal., 1996, Cancer Res. 56:3055-3061, entirely incorporated by reference.In some cases, the scFv can be joined to the Fc region, and may includesome or the entire hinge region.

Human Antibodies

In one embodiment, the antibody is a fully human antibody with at leastone modification as outlined herein. “Fully human antibody” or “completehuman antibody” refers to a human antibody having the gene sequence ofan antibody derived from a human chromosome with the modificationsoutlined herein.

Antibody Fusions

In one embodiment, the antibodies of the invention are antibody fusionproteins (sometimes referred to herein as an “antibody conjugate”). Onetype of antibody fusions comprises Fc fusions, which join the Fc regionwith a conjugate partner. By “Fc fusion” as used herein is meant aprotein wherein one or more polypeptides is operably linked to an Fcregion. Fc fusion is herein meant to be synonymous with the terms“immunoadhesin”, “Ig fusion”, “Ig chimera”, and “receptor globulin”(sometimes with dashes) as used in the prior art (Chamow et al., 1996,Trends Biotechnol 14:52-60; Ashkenazi et al., 1997, Curr Opin Immunol9:195-200, both entirely incorporated by reference). An Fc fusioncombines the Fc region of an immunoglobulin with a fusion partner, whichin general can be any protein or small molecule. Virtually any proteinor small molecule may be linked to Fc to generate an Fc fusion. Proteinfusion partners may include, but are not limited to, the variable regionof any antibody, the target-binding region of a receptor, an adhesionmolecule, a ligand, an enzyme, a cytokine, a chemokine, or some otherprotein or protein domain. Small molecule fusion partners may includeany therapeutic agent that directs the Fc fusion to a therapeutictarget. Such targets may be any molecule, preferably an extracellularreceptor, which is implicated in disease. Thus, the IgG variants can belinked to one or more fusion partners. In one alternate embodiment, theIgG variant is conjugated or operably linked to another therapeuticcompound. The therapeutic compound may be a cytotoxic agent, achemotherapeutic agent, a toxin, a radioisotope, a cytokine, or othertherapeutically active agent. The IgG may be linked to one of a varietyof nonproteinaceous polymers, e.g., polyethylene glycol, polypropyleneglycol, polyoxyalkylenes, or copolymers of polyethylene glycol andpolypropylene glycol.

In addition to Fc fusions, antibody fusions include the fusion of theconstant region of the heavy chain with one or more fusion partners(again including the variable region of any antibody), while otherantibody fusions are substantially or completely full length antibodieswith fusion partners. In one embodiment, a role of the fusion partner isto mediate target binding, and thus it is functionally analogous to thevariable regions of an antibody (and in fact can be). Virtually anyprotein or small molecule may be linked to Fc to generate an Fc fusion(or antibody fusion). Protein fusion partners may include, but are notlimited to, the target-binding region of a receptor, an adhesionmolecule, a ligand, an enzyme, a cytokine, a chemokine, or some otherprotein or protein domain. Small molecule fusion partners may includeany therapeutic agent that directs the Fc fusion to a therapeutictarget. Such targets may be any molecule, preferably an extracellularreceptor, which is implicated in disease.

The conjugate partner can be proteinaceous or non-proteinaceous; thelatter generally being generated using functional groups on the antibodyand on the conjugate partner. For example linkers are known in the art;for example, homo-or hetero-bifunctional linkers as are well known (see,1994 Pierce Chemical Company catalog, technical section oncross-linkers, pages 155-200, incorporated herein by reference).

Suitable conjugates include, but are not limited to, labels as describedbelow, drugs and cytotoxic agents including, but not limited to,cytotoxic drugs (e.g., chemotherapeutic agents) or toxins or activefragments of such toxins. Suitable toxins and their correspondingfragments include diptheria A chain, exotoxin A chain, ricin A chain,abrin A chain, curcin, crotin, phenomycin, enomycin and the like.Cytotoxic agents also include radiochemicals made by conjugatingradioisotopes to antibodies, or binding of a radionuclide to a chelatingagent that has been covalently attached to the antibody. Additionalembodiments utilize calicheamicin, auristatins, geldanamycin,maytansine, and duocarmycins and analogs; for the latter, see U.S.2003/0050331A1, entirely incorporated by reference.

Covalent Modifications of Antibodies

Covalent modifications of antibodies are included within the scope ofthis invention, and are generally, but not always, donepost-translationally. For example, several types of covalentmodifications of the antibody are introduced into the molecule byreacting specific amino acid residues of the antibody with an organicderivatizing agent that is capable of reacting with selected side chainsor the N- or C-terminal residues.

Cysteinyl residues most commonly are reacted with a-haloacetates (andcorresponding amines), such as chloroacetic acid or chloroacetamide, togive carboxymethyl or carboxyamidomethyl derivatives. Cysteinyl residuesmay also be derivatized by reaction with bromotrifluoroacetone,α-bromo-β-(5-imidozoyl)propionic acid, chloroacetyl phosphate,N-alkylmaleimides, 3-nitro-2-pyridyl disulfide, methyl 2-pyridyldisulfide, p-chloromercuribenzoate, 2-chloromercuri-4-nitrophenol, orchloro-7-nitrobenzo-2-oxa-1,3-diazole and the like.

Histidyl residues are derivatized by reaction with diethylpyrocarbonateat pH 5.5-7.0 because this agent is relatively specific for the histidylside chain. Para-bromophenacyl bromide also is useful; the reaction ispreferably performed in 0.1 M sodium cacodylate at pH 6.0.

Lysinyl and amino terminal residues are reacted with succinic or othercarboxylic acid anhydrides. Derivatization with these agents has theeffect of reversing the charge of the lysinyl residues. Other suitablereagents for derivatizing alpha-amino-containing residues includeimidoesters such as methyl picolinimidate; pyridoxal phosphate;pyridoxal; chloroborohydride; trinitrobenzenesulfonic acid;O-methylisourea; 2,4-pentanedione; and transaminase-catalyzed reactionwith glyoxylate.

Arginyl residues are modified by reaction with one or severalconventional reagents, among them phenylglyoxal, 2,3-butanedione,1,2-cyclohexanedione, and ninhydrin. Derivatization of arginine residuesrequires that the reaction be performed in alkaline conditions becauseof the high pKa of the guanidine functional group. Furthermore, thesereagents may react with the groups of lysine as well as the arginineepsilon-amino group.

The specific modification of tyrosyl residues may be made, withparticular interest in introducing spectral labels into tyrosyl residuesby reaction with aromatic diazonium compounds or tetranitromethane. Mostcommonly, N-acetylimidizole and tetranitromethane are used to formO-acetyl tyrosyl species and 3-nitro derivatives, respectively. Tyrosylresidues are iodinated using 125I or 131I to prepare labeled proteinsfor use in radioimmunoassay, the chloramine T method described abovebeing suitable.

Carboxyl side groups (aspartyl or glutamyl) are selectively modified byreaction with carbodiimides (R′—N═C═N—R′), where R and R′ are optionallydifferent alkyl groups, such as 1-cyclohexyl-3-(2-morpholinyl-4-ethyl)carbodiimide or 1-ethyl-3-(4-azonia-4,4-dimethylpentyl) carbodiimide.Furthermore, aspartyl and glutamyl residues are converted to asparaginyland glutaminyl residues by reaction with ammonium ions.

Derivatization with bifunctional agents is useful for crosslinkingantibodies to a water-insoluble support matrix or surface for use in avariety of methods, in addition to methods described below. Commonlyused crosslinking agents include, e.g.,1,1-bis(diazoacetyl)-2-phenylethane, glutaraldehyde,N-hydroxysuccinimide esters, for example, esters with 4-azidosalicylicacid, homobifunctional imidoesters, including disuccinimidyl esters suchas 3,3′-dithiobis (succinimidylpropionate), and bifunctional maleimidessuch as bis-N-maleimido-1,8-octane. Derivatizing agents such asmethyl-3-[(p-azidophenyl)dithio]propioimidate yield photoactivatableintermediates that are capable of forming crosslinks in the presence oflight. Alternatively, reactive water-insoluble matrices such as cyanogenbromide-activated carbohydrates and the reactive substrates described inU.S. Pat. Nos. 3,969,287; 3,691,016; 4,195,128; 4,247,642; 4,229,537;and 4,330,440, all entirely incorporated by reference, are employed forprotein immobilization.

Glutaminyl and asparaginyl residues are frequently deamidated to thecorresponding glutamyl and aspartyl residues, respectively.Alternatively, these residues are deamidated under mildly acidicconditions. Either form of these residues falls within the scope of thisinvention. Other modifications include hydroxylation of proline andlysine, phosphorylation of hydroxyl groups of seryl or threonylresidues, methylation of the a-amino groups of lysine, arginine, andhistidine side chains (T. E. Creighton, Proteins: Structure andMolecular Properties, W. H. Freeman & Co., San Francisco, pp. 79-86[1983], entirely incorporated by reference), acetylation of theN-terminal amine, and amidation of any C-terminal carboxyl group.

Glycosylation

Another type of covalent modification is glycosylation. In anotherembodiment, the IgG variants disclosed herein can be modified to includeone or more engineered glycoforms. By “engineered glycoform” as usedherein is meant a carbohydrate composition that is covalently attachedto an IgG, wherein said carbohydrate composition differs chemically fromthat of a parent IgG. Engineered glycoforms may be useful for a varietyof purposes, including but not limited to enhancing or reducing effectorfunction. Engineered glycoforms may be generated by a variety of methodsknown in the art (Umaüa et al., 1999, Nat Biotechnol 17:176-180; Davieset al., 2001, Biotechnol Bioeng 74:288-294; Shields et al., 2002, J BiolChem 277:26733-26740; Shinkawa et al., 2003, J Biol Chem 278:3466-3473;U.S. Pat. No. 6,602,684; U.S. Ser. No. 10/277,370; U.S. Ser. No.10/113,929; PCT WO 00/61739A1; PCT WO 01/29246A1; PCT WO 02/31140A1; PCTWO 02/30954A1, all entirely incorporated by reference; (Potelligent®technology [Biowa, Inc., Princeton, N.J.]; GlycoMAb® glycosylationengineering technology [Glycart Biotechnology AG, Zurich, Switzerland]).Many of these techniques are based on controlling the level offucosylated and/or bisecting oligosaccharides that are covalentlyattached to the Fc region, for example by expressing an IgG in variousorganisms or cell lines, engineered or otherwise (for example Lec-13 CHOcells or rat hybridoma YB2/0 cells), by regulating enzymes involved inthe glycosylation pathway (for example FUT8 [α1,6-fucosyltranserase]and/or β1-4-N-acetylglucosaminyltransferase III [GnTIII]), or bymodifying carbohydrate(s) after the IgG has been expressed. Engineeredglycoform typically refers to the different carbohydrate oroligosaccharide; thus an IgG variant, for example an antibody or Fcfusion, can include an engineered glycoform. Alternatively, engineeredglycoform may refer to the IgG variant that comprises the differentcarbohydrate or oligosaccharide. As is known in the art, glycosylationpatterns can depend on both the sequence of the protein (e.g., thepresence or absence of particular glycosylation amino acid residues,discussed below), or the host cell or organism in which the protein isproduced. Particular expression systems are discussed below.

Glycosylation of polypeptides is typically either N-linked or O-linked.N-linked refers to the attachment of the carbohydrate moiety to the sidechain of an asparagine residue. The tri-peptide sequencesasparagine-X-serine and asparagine-X-threonine, where X is any aminoacid except proline, are the recognition sequences for enzymaticattachment of the carbohydrate moiety to the asparagine side chain.Thus, the presence of either of these tri-peptide sequences in apolypeptide creates a potential glycosylation site. O-linkedglycosylation refers to the attachment of one of the sugarsN-acetylgalactosamine, galactose, or xylose, to a hydroxyamino acid,most commonly serine or threonine, although 5-hydroxyproline or5-hydroxylysine may also be used.

Addition of glycosylation sites to the antibody is convenientlyaccomplished by altering the amino acid sequence such that it containsone or more of the above-described tri-peptide sequences (for N-linkedglycosylation sites). The alteration may also be made by the additionof, or substitution by, one or more serine or threonine residues to thestarting sequence (for O-linked glycosylation sites). For ease, theantibody amino acid sequence is preferably altered through changes atthe DNA level, particularly by mutating the DNA encoding the targetpolypeptide at preselected bases such that codons are generated thatwill translate into the desired amino acids.

Another means of increasing the number of carbohydrate moieties on theantibody is by chemical or enzymatic coupling of glycosides to theprotein. These procedures are advantageous in that they do not requireproduction of the protein in a host cell that has glycosylationcapabilities for N- and O-linked glycosylation. Depending on thecoupling mode used, the sugar(s) may be attached to (a) arginine andhistidine, (b) free carboxyl groups, (c) free sulfhydryl groups such asthose of cysteine, (d) free hydroxyl groups such as those of serine,threonine, or hydroxyproline, (e) aromatic residues such as those ofphenylalanine, tyrosine, or tryptophan, or (f) the amide group ofglutamine. These methods are described in WO 87/05330 and in Aplin andWriston, 1981, CRC Crit. Rev. Biochem., pp. 259-306, both entirelyincorporated by reference.

Removal of carbohydrate moieties present on the starting antibody may beaccomplished chemically or enzymatically. Chemical deglycosylationrequires exposure of the protein to the compoundtrifluoromethanesulfonic acid, or an equivalent compound. This treatmentresults in the cleavage of most or all sugars except the linking sugar(N-acetylglucosamine or N-acetylgalactosamine), while leaving thepolypeptide intact. Chemical deglycosylation is described by Hakimuddinet al., 1987, Arch. Biochem. Biophys. 259:52 and by Edge et al., 1981,Anal. Biochem. 118:131, both entirely incorporated by reference.Enzymatic cleavage of carbohydrate moieties on polypeptides can beachieved by the use of a variety of endo- and exo-glycosidases asdescribed by Thotakura et al., 1987, Meth. Enzymol. 138:350, entirelyincorporated by reference. Glycosylation at potential glycosylationsites may be prevented by the use of the compound tunicamycin asdescribed by Duskin et al., 1982, J. Biol. Chem. 257:3105, entirelyincorporated by reference. Tunicamycin blocks the formation ofprotein-N-glycoside linkages.

Another type of covalent modification of the antibody comprises linkingthe antibody to various nonproteinaceous polymers, including, but notlimited to, various polyols such as polyethylene glycol, polypropyleneglycol or polyoxyalkylenes, in the manner set forth in, for example,2005-2006 PEG Catalog from Nektar Therapeutics (available at the Nektarwebsite) U.S. Pat. Nos. 4,640,835; 4,496,689; 4,301,144; 4,670,417;4,791,192 or 4,179,337, all entirely incorporated by reference. Inaddition, as is known in the art, amino acid substitutions may be madein various positions within the antibody to facilitate the addition ofpolymers such as PEG. See for example, U.S. Publication No.2005/0114037A1, entirely incorporated by reference.

Labeled Antibodies

In some embodiments, the covalent modification of the antibodies of theinvention comprises the addition of one or more labels. In some cases,these are considered antibody fusions. The term “labelling group” meansany detectable label. In some embodiments, the labelling group iscoupled to the antibody via spacer arms of various lengths to reducepotential steric hindrance. Various methods for labelling proteins areknown in the art and may be used in performing the present invention.

In general, labels fall into a variety of classes, depending on theassay in which they are to be detected: a) isotopic labels, which may beradioactive or heavy isotopes; b) magnetic labels (e.g., magneticparticles); c) redox active moieties; d) optical dyes; enzymatic groups(e.g. horseradish peroxidase, β-galactosidase, luciferase, alkalinephosphatase); e) biotinylated groups; and f) predetermined polypeptideepitopes recognized by a secondary reporter (e.g., leucine zipper pairsequences, binding sites for secondary antibodies, metal bindingdomains, epitope tags, etc.). In some embodiments, the labelling groupis coupled to the antibody via spacer arms of various lengths to reducepotential steric hindrance. Various methods for labelling proteins areknown in the art and may be used in performing the present invention.

Specific labels include optical dyes, including, but not limited to,chromophores, phosphors and fluorophores, with the latter being specificin many instances. Fluorophores can be either “small molecule” fluores,or proteinaceous fluores.

By “fluorescent label” is meant any molecule that may be detected viaits inherent fluorescent properties. Suitable fluorescent labelsinclude, but are not limited to, fluorescein, rhodamine,tetramethylrhodamine, eosin, erythrosin, coumarin, methyl-coumarins,pyrene, Malacite green, stilbene, Lucifer Yellow, Cascade BlueJ, TexasRed, IAEDANS, EDANS, BODIPY FL, LC Red 640, Cy 5, Cy 5.5, LC Red 705,Oregon green, the Alexa-Fluor dyes (Alexa Fluor 350, Alexa Fluor 430,Alexa Fluor 488, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594,Alexa Fluor 633, Alexa Fluor 660, Alexa Fluor 680), Cascade Blue,Cascade Yellow and R-phycoerythrin (PE) (Molecular Probes, Eugene,Oreg.), FITC, Rhodamine, and Texas Red (Pierce, Rockford, Ill.), Cy5,Cy5.5, Cy7 (Amersham Life Science, Pittsburgh, Pa.). Suitable opticaldyes, including fluorophores, are described in Molecular Probes Handbookby Richard P. Haugland, entirely incorporated by reference.

Suitable proteinaceous fluorescent labels also include, but are notlimited to, green fluorescent protein, including a Renilla, Ptilosarcus,or Aequorea species of GFP (Chalfie et al., 1994, Science 263:802-805),EGFP (Clontech Laboratories, Inc., Genbank Accession Number U55762),blue fluorescent protein (BFP, Quantum Biotechnologies, Inc. 1801 deMaisonneuve Blvd. West, 8th Floor, Montreal, Quebec, Canada H3H 1J9;Stauber, 1998, Biotechniques 24:462-471; Heim et al., 1996, Curr. Biol.6:178-182), enhanced yellow fluorescent protein (EYFP, ClontechLaboratories, Inc.), luciferase (Ichiki et al., 1993, J. Immunol.150:5408-5417), β galactosidase (Nolan et al., 1988, Proc. Natl. Acad.Sci. U.S.A. 85:2603-2607) and Renilla (WO92/15673, WO95/07463,WO98/14605, WO98/26277, WO99/49019, U.S. Pat. Nos. 5,292,658, 5,418,155,5,683,888, 5,741,668, 5,777,079, 5,804,387, 5,874,304, 5,876,995,5,925,558). All of the above-cited references in this paragraph areexpressly incorporated herein by reference.

IgG Variants

In one embodiment, the invention provides variant IgG proteins. At aminimum, IgG variants comprise an antibody fragment comprising theCH2-CH3 region of the heavy chain. In addition, suitable IgG variantscomprise Fc domains (e.g. including the lower hinge region), as well asIgG variants comprising the constant region of the heavy chain(CH1-hinge-CH2-CH3) also being useful in the present invention, all ofwhich can be fused to fusion partners.

An IgG variant includes one or more amino acid modifications relative toa parent IgG polypeptide, in some cases relative to the wild type IgG.The IgG variant can have one or more optimized properties. An IgGvariant differs in amino acid sequence from its parent IgG by virtue ofat least one amino acid modification. Thus IgG variants have at leastone amino acid modification compared to the parent. Alternatively, theIgG variants may have more than one amino acid modification as comparedto the parent, for example from about one to fifty amino acidmodifications, preferably from about one to ten amino acidmodifications, and most preferably from about one to about five aminoacid modifications compared to the parent.

Thus the sequences of the IgG variants and those of the parent Fcpolypeptide are substantially homologous. For example, the variant IgGvariant sequences herein will possess about 80% homology with the parentIgG variant sequence, preferably at least about 90% homology, and mostpreferably at least about 95% homology. Modifications may be madegenetically using molecular biology, or may be made enzymatically orchemically.

Target Antigens for Antibodies

Virtually any antigen may be targeted by the IgG variants, including butnot limited to proteins, subunits, domains, motifs, and/or epitopesbelonging to the following list of target antigens, which includes bothsoluble factors such as cytokines and membrane-bound factors, includingtransmembrane receptors: 17-IA, 4-1BB, 4Dc, 6-keto-PGF1a, 8-iso-PGF2a,8-oxo-dG, A1 Adenosine Receptor, A33, ACE, ACE-2, Activin, Activin A,Activin AB, Activin B, Activin C, Activin RIA, Activin RIA ALK-2,Activin RIB ALK-4, Activin RIIA, Activin RIIB, ADAM, ADAM10, ADAM12,ADAM15, ADAM17/TACE, ADAMS, ADAM9, ADAMTS, ADAMTS4, ADAMTS5, Addressins,aFGF, ALCAM, ALK, ALK-1, ALK-7, alpha-1-antitrypsin, alpha-V/beta-1antagonist, ANG, Ang, APAF-1, APE, APJ, APP, APRIL, AR, ARC, ART,Artemin, anti-Id, ASPARTIC, Atrial natriuretic factor, av/b3 integrin,Axl, b2M, B7-1, B7-2, B7-H, B-lymphocyte Stimulator (BlyS), BACE,BACE-1, Bad, BAFF, BAFF-R, Bag-1, BAK, Bax, BCA-1, BCAM, Bcl, BCMA,BDNF, b-ECGF, bFGF, BID, Bik, BIM, BLC, BL-CAM, BLK, BMP, BMP-2 BMP-2a,BMP-3 Osteogenin, BMP-4 BMP-2b, BMP-5, BMP-6 Vgr-1, BMP-7 (OP-1), BMP-8(BMP-8a, OP-2), BMPR, BMPR-IA (ALK-3), BMPR-IB (ALK-6), BRK-2, RPK-1,BMPR-II (BRK-3), BMPs, b-NGF, BOK, Bombesin, Bone-derived neurotrophicfactor, BPDE, BPDE-DNA, BTC, complement factor 3 (C3), C3a, C4, C5, C5a,C10, CA125, CAD-8, Calcitonin, cAMP, carcinoembryonic antigen (CEA),carcinoma-associated antigen, Cathepsin A, Cathepsin B, CathepsinC/DPPI, Cathepsin D, Cathepsin E, Cathepsin H, Cathepsin L, Cathepsin O,Cathepsin S, Cathepsin V, Cathepsin X/Z/P, CBL, CCI, CCK2, CCL, CCL1,CCL11, CCL12, CCL13, CCL14, CCL15, CCL16, CCL17, CCL18, CCL19, CCL2,CCL20, CCL21, CCL22, CCL23, CCL24, CCL25, CCL26, CCL27, CCL28, CCL3,CCL4, CCL5, CCL6, CCL7, CCL8, CCL9/10, CCR, CCR1, CCR10, CCR10, CCR2,CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD1, CD2, CD3, CD3E, CD4, CD5,CD6, CD7, CD8, CD10, CD11a, CD11b, CD11c, CD13, CD14, CD15, CD16, CD18,CD19, CD20, CD21, CD22, CD23, CD25, CD27L, CD28, CD29, CD30, CD30L,CD32, CD33 (p67 proteins), CD34, CD38, CD40, CD40L, CD44, CD45, CD46,CD49a, CD52, CD54, CD55, CD56, CD61, CD64, CD66e, CD74, CD80 (B7-1),CD89, CD95, CD123, CD137, CD138, CD140a, CD146, CD147, CD148, CD152,CD164, CEACAM5, CFTR, cGMP, CINC, Clostridium botulinum toxin,Clostridium perfringens toxin, CKb8-1, CLC, CMV, CMV UL, CNTF, CNTN-1,COX, C-Ret, CRG-2, CT-1, CTACK, CTGF, CTLA-4, CX3CL1, CX3CR1, CXCL,CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6, CXCL7, CXCL8, CXCL9, CXCL10,CXCL11, CXCL12, CXCL13, CXCL14, CXCL15, CXCL16, CXCR, CXCR1, CXCR2,CXCR3, CXCR4, CXCR5, CXCR6, cytokeratin tumor-associated antigen, DAN,DCC, DcR3, DC-SIGN, Decay accelerating factor, des(1-3)-IGF-I (brainIGF-1), Dhh, digoxin, DNAM-1, Dnase, Dpp, DPPIV/CD26, Dtk, ECAD, EDA,EDA-A1, EDA-A2, EDAR, EGF, EGFR (ErbB-1), EMA, EMMPRIN, ENA, endothelinreceptor, Enkephalinase, eNOS, Eot, eotaxin1, EpCAM, Ephrin B2/EphB4,EPO, ERCC, E-selectin, ET-1, Factor IIa, Factor VII, Factor VIIIc,Factor IX, fibroblast activation protein (FAP), Fas, FcR1, FEN-1,Ferritin, FGF, FGF-19, FGF-2, FGF3, FGF-8, FGFR, FGFR-3, Fibrin, FL,FLIP, Flt-3, Flt-4, Follicle stimulating hormone, Fractalkine, FZD1,FZD2, FZD3, FZD4, FZD5, FZD6, FZD7, FZD8, FZD9, FZD10, G250, Gas 6,GCP-2, GCSF, GD2, GD3, GDF, GDF-1, GDF-3 (Vgr-2), GDF-5 (BMP-14,CDMP-1), GDF-6 (BMP-13, CDMP-2), GDF-7 (BMP-12, CDMP-3), GDF-8(Myostatin), GDF-9, GDF-15 (MIC-1), GDNF, GDNF, GFAP, GFRa-1,GFR-alpha1, GFR-alpha2, GFR-alpha3, GITR, Glucagon, Glut 4, glycoproteinIIb/IIIa (GP IIb/IIIa), GM-CSF, gp130, gp72, GRO, Growth hormonereleasing factor, Hapten (NP-cap or NIP-cap), HB-EGF, HCC, HCMV gBenvelope glycoprotein, HCMV) gH envelope glycoprotein, HCMV UL,Hemopoietic growth factor (HGF), Hep B gp120, heparanase, Her2, Her2/neu(ErbB-2), Her3 (ErbB-3), Her4 (ErbB-4), herpes simplex virus (HSV) gBglycoprotein, HSV gD glycoprotein, HGFA, High molecular weightmelanoma-associated antigen (HMW-MAA), HIV gp120, HIV IIIB gp 120 V3loop, HLA, HLA-DR, HM1.24, HMFG PEM, HRG, Hrk, human cardiac myosin,human cytomegalovirus (HCMV), human growth hormone (HGH), HVEM, I-309,IAP, ICAM, ICAM-1, ICAM-3, ICE, ICOS, IFNg, Ig, IgA receptor, IgE, IGF,IGF binding proteins, IGF-1R, IGFBP, IGF-I, IGF-II, IL, IL-1, IL-1R,IL-2, IL-2R, IL-4, IL-4R, IL-5, IL-5R, IL-6, IL-6R, IL-8, IL-9, IL-10,IL-12, IL-13, IL-15, IL-18, IL-18R, IL-23, interferon (INF)-alpha,INF-beta, INF-gamma, Inhibin, iNOS, Insulin A-chain, Insulin B-chain,Insulin-like growth factor 1, integrin alpha2, integrin alpha3, integrinalpha4, integrin alpha4/beta1, integrin alpha4/beta7, integrin alpha5(alphaV), integrin alpha5/beta1, integrin alpha5/beta3, integrin alpha6,integrin beta1, integrin beta2, interferon gamma, IP-10, I-TAC, JE,Kallikrein 2, Kallikrein 5, Kallikrein 6, Kallikrein 11, Kallikrein 12,Kallikrein 14, Kallikrein 15, Kallikrein L1, Kallikrein L2, KallikreinL3, Kallikrein L4, KC, KDR, Keratinocyte Growth Factor (KGF), laminin 5,LAMP, LAP, LAP (TGF-1), Latent TGF-1, Latent TGF-1 bp1, LBP, LDGF,LECT2, Lefty, Lewis-Y antigen, Lewis-Y related antigen, LFA-1, LFA-3,Lfo, LIF, LIGHT, lipoproteins, LIX, LKN, Lptn, L-Selectin, LT-a, LT-b,LTB4, LTBP-1, Lung surfactant, Luteinizing hormone, Lymphotoxin BetaReceptor, Mac-1, MAdCAM, MAG, MAP2, MARC, MCAM, MCAM, MCK-2, MCP, M-CSF,MDC, Mer, METALLOPROTEASES, MGDF receptor, MGMT, MHC (HLA-DR), MIF, MIG,MIP, MIP-1-alpha, MK, MMAC1, MMP, MMP-1, MMP-10, MMP-11, MMP-12, MMP-13,MMP-14, MMP-15, MMP-2, MMP-24, MMP-3, MMP-7, MMP-8, MMP-9, MPIF, Mpo,MSK, MSP, mucin (Muc1), MUC18, Muellerian-inhibitin substance, Mug,MuSK, NAIP, NAP, NCAD, N-Cadherin, NCA 90, NCAM, NCAM, Neprilysin,Neurotrophin-3,-4, or -6, Neurturin, Neuronal growth factor (NGF), NGFR,NGF-beta, nNOS, NO, NOS, Npn, NRG-3, NT, NTN, OB, OGG1, OPG, OPN, OSM,OX40L, OX40R, p150, p95, PADPr, Parathyroid hormone, PARC, PARP, PBR,PBSF, PCAD, P-Cadherin, PCNA, PDGF, PDGF, PDK-1, PECAM, PEM, PF4, PGE,PGF, PGI2, PGJ2, PIN, PLA2, placental alkaline phosphatase (PLAP), PIGF,PLP, PP14, Proinsulin, Prorelaxin, Protein C, PS, PSA, PSCA, prostatespecific membrane antigen (PSMA), PTEN, PTHrp, Ptk, PTN, R51, RANK,RANKL, RANTES, RANTES, Relaxin A-chain, Relaxin B-chain, renin,respiratory syncytial virus (RSV) F, RSV Fgp, Ret, Rheumatoid factors,RLIP76, RPA2, RSK, S100, SCF/KL, SDF-1, SERINE, Serum albumin, sFRP-3,Shh, SIGIRR, SK-1, SLAM, SLPI, SMAC, SMDF, SMOH, SOD, SPARC, Stat,STEAP, STEAP-II, TACE, TACI, TAG-72 (tumor-associated glycoprotein-72),TARC, TCA-3, T-cell receptors (e.g., T-cell receptor alpha/beta), TdT,TECK, TEM1, TEM5, TEM7, TEM8, TERT, testicular PLAP-like alkalinephosphatase, TfR, TGF, TGF-alpha, TGF-beta, TGF-beta Pan Specific,TGF-beta RI (ALK-5), TGF-beta RII, TGF-beta RIIb, TGF-beta RIII,TGF-beta1, TGF-beta2, TGF-beta3, TGF-beta4, TGF-beta5, Thrombin, ThymusCk-1, Thyroid stimulating hormone, Tie, TIMP, TIQ, Tissue Factor,TMEFF2, Tmpo, TMPRSS2, TNF, TNF-alpha, TNF-alpha beta, TNF-beta2, TNFc,TNF-RI, TNF-RII, TNFRSF10A (TRAIL R1 Apo-2, DR4), TNFRSF10B (TRAIL R2DRS, KILLER, TRICK-2A, TRICK-B), TNFRSF10C (TRAIL R3 DcR1, LIT, TRID),TNFRSF10D (TRAIL R4 DcR2, TRUNDD), TNFRSF11A (RANK ODF R, TRANCE R),TNFRSF11B (OPG OCIF, TR1), TNFRSF12 (TWEAK R FN14), TNFRSF13B (TACI),TNFRSF13C (BAFF R), TNFRSF14 (HVEM ATAR, HveA, LIGHT R, TR2), TNFRSF16(NGFR p75NTR), TNFRSF17 (BCMA), TNFRSF18 (GITR AITR), TNFRSF19 (TROYTAJ, TRADE), TNFRSF19L (RELT), TNFRSF1A (TNF RI CD120a, p55-60),TNFRSF1B (TNF RII CD120b, p75-80), TNFRSF26 (TNFRH3), TNFRSF3 (LTbR TNFRIII, TNFC R), TNFRSF4 (OX40 ACT35, TXGP1 R), TNFRSFS (CD40 p50),TNFRSF6 (Fas Apo-1, APT1, CD95), TNFRSF6B (DcR3 M68, TR6), TNFRSF7(CD27), TNFRSF8 (CD30), TNFRSF9 (4-1BB CD137, ILA), TNFRSF21 (DR6),TNFRSF22 (DcTRAIL R2 TNFRH2), TNFRST23 (DcTRAIL R1 TNFRH1), TNFRSF25(DR3 Apo-3, LARD, TR-3, TRAMP, WSL-1), TNFSF10 (TRAIL Apo-2 Ligand,TL2), TNFSF11 (TRANCE/RANK Ligand ODF, OPG Ligand), TNFSF12 (TWEAK Apo-3Ligand, DR3 Ligand), TNFSF13 (APRIL TALL2), TNFSF13B (BAFF BLYS, TALL1,THANK, TNFSF20), TNFSF14 (LIGHT HVEM Ligand, LTg), TNFSF15 (TL1A/VEGI),TNFSF18 (GITR Ligand AITR Ligand, TL6), TNFSF1A (TNF-a Conectin, DIF,TNFSF2), TNFSF1B (TNF-b LTa, TNFSF1), TNFSF3 (LTb TNFC, p33), TNFSF4(OX40 Ligand gp34, TXGP1), TNFSF5 (CD40 Ligand CD154, gp39, HIGM1, IMD3,TRAP), TNFSF6 (Fas Ligand Apo-1 Ligand, APT1 Ligand), TNFSF7 (CD27Ligand CD70), TNFSF8 (CD30 Ligand CD153), TNFSF9 (4-1BB Ligand CD137Ligand), TP-1, t-PA, Tpo, TRAIL, TRAIL R, TRAIL-R1, TRAIL-R2, TRANCE,transferring receptor, TRF, Trk, TROP-2, TSG, TSLP, tumor-associatedantigen CA 125, tumor-associated antigen expressing Lewis Y relatedcarbohydrate, TWEAK, TXB2, Ung, uPAR, uPAR-1, Urokinase, VCAM, VCAM-1,VECAD, VE-Cadherin, VE-cadherin-2, VEFGR-1 (fit-1), VEGF, VEGFR, VEGFR-3(flt-4), VEGI, VIM, Viral antigens, VLA, VLA-1, VLA-4, VNR integrin, vonWillebrands factor, WIF-1, WNT1, WNT2, WNT2B/13, WNT3, WNT3A, WNT4,WNT5A, WNT5B, WNT6, WNT7A, WNT7B, WNT8A, WNT8B, WNT9A, WNT9A, WNT9B,WNT10A, WNT10B, WNT11, WNT16, XCL1, XCL2, XCR1, XCR1, XEDAR, XIAP, XPD,and receptors for hormones and growth factors.

One skilled in the art will appreciate that the aforementioned list oftargets refers not only to specific proteins and biomolecules, but thebiochemical pathway or pathways that comprise them. For example,reference to CTLA-4 as a target antigen implies that the ligands andreceptors that make up the T cell co-stimulatory pathway, includingCTLA-4, B7-1, B7-2, CD28, and any other undiscovered ligands orreceptors that bind these proteins, are also targets. Thus target asused herein refers not only to a specific biomolecule, but the set ofproteins that interact with said target and the members of thebiochemical pathway to which said target belongs. One skilled in the artwill further appreciate that any of the aforementioned target antigens,the ligands or receptors that bind them, or other members of theircorresponding biochemical pathway, may be operably linked to the Fcvariants of the present invention in order to generate an Fc fusion.Thus for example, an Fc fusion that targets EGFR could be constructed byoperably linking an Fc variant to EGF, TGF-b, or any other ligand,discovered or undiscovered, that binds EGFR. Accordingly, an Fc variantof the present invention could be operably linked to EGFR in order togenerate an Fc fusion that binds EGF, TGF-b, or any other ligand,discovered or undiscovered, that binds EGFR. Thus virtually anypolypeptide, whether a ligand, receptor, or some other protein orprotein domain, including but not limited to the aforementioned targetsand the proteins that compose their corresponding biochemical pathways,may be operably linked to the Fc variants of the present invention todevelop an Fc fusion.

The choice of suitable antigen depends on the desired application. Foranti-cancer treatment it is desirable to have a target whose expressionis restricted to the cancerous cells. Some targets that have provenespecially amenable to antibody therapy are those with signalingfunctions. Other therapeutic antibodies exert their effects by blockingsignaling of the receptor by inhibiting the binding between a receptorand its cognate ligand. Another mechanism of action of therapeuticantibodies is to cause receptor down regulation. Other antibodies do notwork by signaling through their target antigen. In some cases,antibodies directed against infectious disease agents are used.

In one embodiment, the Fc variants of the present invention areincorporated into an antibody against a cytokine. Alternatively, the Fcvariants are fused or conjugated to a cytokine. By “cytokine” as usedherein is meant a generic term for proteins released by one cellpopulation that act on another cell as intercellular mediators. Forexample, as described in Penichet et al., 2001, J Immunol Methods248:91-101, expressly incorporated by reference, cytokines may be fusedto antibody to provide an array of desirable properties. Examples ofsuch cytokines are lymphokines, monokines, and traditional polypeptidehormones. Included among the cytokines are growth hormone such as humangrowth hormone, N-methionyl human growth hormone, and bovine growthhormone; parathyroid hormone; thyroxine; insulin; proinsulin; relaxin;prorelaxin; glycoprotein hormones such as follicle stimulating hormone(FSH), thyroid stimulating hormone (TSH), and luteinizing hormone (LH);hepatic growth factor; fibroblast growth factor; prolactin; placentallactogen; tumor necrosis factor-alpha and -beta; mullerian-inhibitingsubstance; mouse gonadotropin-associated peptide; inhibin; activin;vascular endothelial growth factor; integrin; thrombopoietin (TPO);nerve growth factors such as NGF-beta; platelet-growth factor;transforming growth factors (TGFs) such as TGF-alpha and TGF-beta;insulin-like growth factor-I and -II; erythropoietin (EPO);osteoinductive factors; interferons such as interferon-alpha, beta, and-gamma; colony stimulating factors (CSFs) such as macrophage-CSF(M-CSF); granulocyte-macrophage-CSF (GM-CSF); and granulocyte-CSF(G-CSF); interleukins (ILs) such as IL-1, IL-1 alpha, IL-2, IL-3, IL-4,IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12; IL-15, a tumornecrosis factor such as TNF-alpha or TNF-beta; C5a; and otherpolypeptide factors including LIF and kit ligand (KL). As used herein,the term cytokine includes proteins from natural sources or fromrecombinant cell culture, and biologically active equivalents of thenative sequence cytokines.

Cytokines and soluble targets, such as TNF superfamily members, arepreferred targets for use with the variants of the present invention.For example, anti-VEGF, anti-CTLA-4, and anti-TNF antibodies, orfragments thereof, are particularly good antibodies for the use of Fcvariants that increase the FcRn binding. Therapeutics against thesetargets are frequently involved in the treatment of autoimmune diseasesand require multiple injections over long time periods. Therefore,longer serum half-lives and less frequent treatments, brought about fromthe variants of the present invention, are particularly preferred.

A number of antibodies and Fc fusions that are approved for use, inclinical trials, or in development may benefit from the Fc variants ofthe present invention. These antibodies and Fc fusions are hereinreferred to as “clinical products and candidates”. Thus in a preferredembodiment, the Fc polypeptides of the present invention may find use ina range of clinical products and candidates. For example, a number ofantibodies that target CD20 may benefit from the Fc polypeptides of thepresent invention. For example the Fc polypeptides of the presentinvention may find use in an antibody that is substantially similar torituximab (Rituxan®, IDEC/Genentech/Roche) (see for example U.S. Pat.No. 5,736,137), a chimeric anti-CD20 antibody approved to treatNon-Hodgkin's lymphoma; HuMax-CD20, an anti-CD20 currently beingdeveloped by Genmab, an anti-CD20 antibody described in U.S. Pat. No.5,500,362, AME-133 (Applied Molecular Evolution), hA20 (Immunomedics,Inc.), HumaLYM (Intracel), and PRO70769 (PCT/US2003/040426, entitled“Immunoglobulin Variants and Uses Thereof”). A number of antibodies thattarget members of the family of epidermal growth factor receptors,including EGFR (ErbB-1), Her2/neu (ErbB-2), Her3 (ErbB-3), Her4(ErbB-4), may benefit from the Fc polypeptides of the present invention.For example the Fc polypeptides of the present invention may find use inan antibody that is substantially similar to trastuzumab (Herceptin®,Genentech) (see for example U.S. Pat. No. 5,677,171), a humanizedanti-Her2/neu antibody approved to treat breast cancer; pertuzumab(rhuMab-2C4, Omnitarg™), currently being developed by Genentech; ananti-Her2 antibody described in U.S. Pat. No. 4,753,894; cetuximab(Erbitux®, Imclone) (U.S. Pat. No. 4,943,533; PCT WO 96/40210), achimeric anti-EGFR antibody in clinical trials for a variety of cancers;ABX-EGF (U.S. Pat. No. 6,235,883), currently being developed byAbgenix-Immunex-Amgen; HuMax-EGFr (U.S. Ser. No. 10/172,317), currentlybeing developed by Genmab; 425, EMD55900, EMD62000, and EMD72000 (MerckKGaA) (U.S. Ser. No. 5,558,864; Murthy et al. 1987, Arch BiochemBiophys. 252(2):549-60; Rodeck et al., 1987, J Cell Biochem.35(4):315-20; Kettleborough et al., 1991, Protein Eng. 4(7):773-83);ICR62 (Institute of Cancer Research) (PCT WO 95/20045; Modjtahedi etal., 1993, J. Cell Biophys. 1993, 22(1-3):129-46; Modjtahedi et al.,1993, Br J Cancer. 1993, 67(2):247-53; Modjtahedi et al, 1996, Br JCancer, 73(2):228-35; Modjtahedi et al, 2003, Int J Cancer,105(2):273-80); TheraCIM hR3 (YM Biosciences, Canada and Centro deImmunologia Molecular, Cuba (U.S. Pat. Nos. 5,891,996; 6,506,883; Mateoet al, 1997, Immunotechnology, 3(1):71-81); mAb-806 (Ludwig Institue forCancer Research, Memorial Sloan-Kettering) (Jungbluth et al. 2003, ProcNatl Acad Sci USA. 100(2):639-44); KSB-102 (KS Biomedix); MR1-1 (IVAX,National Cancer Institute) (PCT WO 0162931A2); and SC100 (Scancell) (PCTWO 01/88138). In another preferred embodiment, the Fc polypeptides ofthe present invention may find use in alemtuzumab (Campath®, Millenium),a humanized monoclonal antibody currently approved for treatment ofB-cell chronic lymphocytic leukemia. The Fc polypeptides of the presentinvention may find use in a variety of antibodies or Fc fusions that aresubstantially similar to other clinical products and candidates,including but not limited to muromonab-CD3 (Orthoclone OKT3®), ananti-CD3 antibody developed by Ortho Biotech/Johnson & Johnson,ibritumomab tiuxetan (Zevalin®), an anti-CD20 antibody developed byIDEC/Schering AG, gemtuzumab ozogamicin (Mylotarg®), an anti-CD33 (p67protein) antibody developed by Celltech/Wyeth, alefacept (Amevive®), ananti-LFA-3 Fc fusion developed by Biogen), abciximab (ReoPro®),developed by Centocor/Lilly, basiliximab (Simulect®), developed byNovartis, palivizumab (Synagis®), developed by MedImmune, infliximab(Remicade®), an anti-TNFalpha antibody developed by Centocor, adalimumab(Humira®), an anti-TNFalpha antibody developed by Abbott, Humicade™, ananti-TNFalpha antibody developed by Celltech, etanercept (Enbrel®), ananti-TNFalpha Fc fusion developed by Immunex/Amgen, ABX-CBL, ananti-CD147 antibody being developed by Abgenix, ABX-IL8, an anti-IL8antibody being developed by Abgenix, ABX-MA1, an anti-MUC18 antibodybeing developed by Abgenix, Pemtumomab (R1549, 90Y-muHMFG1), ananti-MUC1 In development by Antisoma, Therex (R1550), an anti-MUC1antibody being developed by Antisoma, AngioMab (AS1405), being developedby Antisoma, HuBC-1, being developed by Antisoma, Thioplatin (AS1407)being developed by Antisoma, Antegren® (natalizumab), ananti-alpha-4-beta-1 (VLA-4) and alpha-4-beta-7 antibody being developedby Biogen, VLA-1 mAb, an anti-VLA-1 integrin antibody being developed byBiogen, LTBR mAb, an anti-lymphotoxin beta receptor (LTBR) antibodybeing developed by Biogen, CAT-152, an anti-TGF-β2 antibody beingdeveloped by Cambridge Antibody Technology, J695, an anti-IL-12 antibodybeing developed by Cambridge Antibody Technology and Abbott, CAT-192, ananti-TGFβ1 antibody being developed by Cambridge Antibody Technology andGenzyme, CAT-213, an anti-Eotaxin 1 antibody being developed byCambridge Antibody Technology, LymphoStat-B™ an anti-Blys antibody beingdeveloped by Cambridge Antibody Technology and Human Genome SciencesInc., TRAIL-R1mAb, an anti-TRAIL-R1 antibody being developed byCambridge Antibody Technology and Human Genome Sciences, Inc., Avastin™(bevacizumab, rhuMAb-VEGF), an anti-VEGF antibody being developed byGenentech, an anti-HER receptor family antibody being developed byGenentech, Anti-Tissue Factor (ATF), an anti-Tissue Factor antibodybeing developed by Genentech, Xolair™ (Omalizumab), an anti-IgE antibodybeing developed by Genentech, Raptiva™ (Efalizumab), an anti-CD11aantibody being developed by Genentech and Xoma, MLN-02 Antibody(formerly LDP-02), being developed by Genentech and MilleniumPharmaceuticals, HuMax CD4, an anti-CD4 antibody being developed byGenmab, HuMax-IL15, an anti-IL15 antibody being developed by Genmab andAmgen, HuMax-Inflam, being developed by Genmab and Medarex,HuMax-Cancer, an anti-Heparanase I antibody being developed by Genmaband Medarex and Oxford GcoSciences, HuMax-Lymphoma, being developed byGenmab and Amgen, HuMax-TAC, being developed by Genmab, IDEC-131, andanti-CD40L antibody being developed by IDEC Pharmaceuticals, IDEC-151(Clenoliximab), an anti-CD4 antibody being developed by IDECPharmaceuticals, IDEC-114, an anti-CD80 antibody being developed by IDECPharmaceuticals, IDEC-152, an anti-CD23 being developed by IDECPharmaceuticals, anti-macrophage migration factor (MIF) antibodies beingdeveloped by IDEC Pharmaceuticals, BEC2, an anti-idiotypic antibodybeing developed by Imclone, IMC-1C11, an anti-KDR antibody beingdeveloped by Imclone, DC101, an anti-flk-1 antibody being developed byImclone, anti-VE cadherin antibodies being developed by Imclone,CEA-Cide™ (labetuzumab), an anti-carcinoembryonic antigen (CEA) antibodybeing developed by Immunomedics, LymphoCide™ (Epratuzumab), an anti-CD22antibody being developed by Immunomedics, AFP-Cide, being developed byImmunomedics, MyelomaCide, being developed by Immunomedics, LkoCide,being developed by Immunomedics, ProstaCide, being developed byImmunomedics, MDX-010, an anti-CTLA4 antibody being developed byMedarex, MDX-060, an anti-CD30 antibody being developed by Medarex,MDX-070 being developed by Medarex, MDX-018 being developed by Medarex,Osidem™ (IDM-1), and anti-Her2 antibody being developed by Medarex andImmuno-Designed Molecules, HuMax™-CD4, an anti-CD4 antibody beingdeveloped by Medarex and Genmab, HuMax-IL15, an anti-IL15 antibody beingdeveloped by Medarex and Genmab, CNTO 148, an anti-TNFα antibody beingdeveloped by Medarex and Centocor/J&J, CNTO 1275, an anti-cytokineantibody being developed by Centocor/J&J, MOR101 and MOR102,anti-intercellular adhesion molecule-1 (ICAM-1) (CD54) antibodies beingdeveloped by MorphoSys, MOR201, an anti-fibroblast growth factorreceptor 3 (FGFR-3) antibody being developed by MorphoSys, Nuvion®(visilizumab), an anti-CD3 antibody being developed by Protein DesignLabs, HuZAF™, an anti-gamma interferon antibody being developed byProtein Design Labs, Anti-α5β1 Integrin, being developed by ProteinDesign Labs, anti-IL-12, being developed by Protein Design Labs, ING-1,an anti-Ep-CAM antibody being developed by Xoma, and MLN01, ananti-Beta2 integrin antibody being developed by Xoma, all of theabove-cited references in this paragraph are expressly incorporatedherein by reference.

The Fc polypeptides of the present invention may be incorporated intothe aforementioned clinical candidates and products, or into antibodiesand Fc fusions that are substantially similar to them. The Fcpolypeptides of the present invention may be incorporated into versionsof the aforementioned clinical candidates and products that arehumanized, affinity matured, engineered, or modified in some other way.

In one embodiment, the Fc polypeptides of the present invention are usedfor the treatment of autoimmune, inflammatory, or transplantindications. Target antigens and clinical products and candidates thatare relevant for such diseases include but are not limited to anti-α4β7integrin antibodies such as LDP-02, anti-beta2 integrin antibodies suchas LDP-01, anti-complement (C5) antibodies such as 5G1.1, anti-CD2antibodies such as BTI-322, MEDI-507, anti-CD3 antibodies such as OKT3,SMART anti-CD3, anti-CD4 antibodies such as IDEC-151, MDX-CD4, OKT4A,anti-CD11a antibodies, anti-CD14 antibodies such as IC14, anti-CD18antibodies, anti-CD23 antibodies such as IDEC 152, anti-CD25 antibodiessuch as Zenapax, anti-CD40L antibodies such as 5c8, Antova, IDEC-131,anti-CD64 antibodies such as MDX-33, anti-CD80 antibodies such asIDEC-114, anti-CD147 antibodies such as ABX-CBL, anti-E-selectinantibodies such as CDP850, anti-gpIIb/IIIa antibodies such asReoPro/Abcixima, anti-ICAM-3 antibodies such as ICM3, anti-ICEantibodies such as VX-740, anti-FcR1 antibodies such as MDX-33, anti-IgEantibodies such as rhuMab-E25, anti-IL-4 antibodies such as SB-240683,anti-IL-5 antibodies such as SB-240563, SCH55700, anti-IL-8 antibodiessuch as ABX-IL8, anti-interferon gamma antibodies, anti-TNF (TNF, TNFa,TNFa, TNF-alpha) antibodies such as CDP571, CDP870, D2E7, Infliximab,MAK-195F, and anti-VLA-4 antibodies such as Antegren.

Fc variants of the present invention such as those with increasedbinding to FcRn may be utilized in TNF inhibitor molecules to provideenhanced properties. Useful TNF inhibitor molecules include any moleculethat inhibits the action of TNF-alpha in a mammal. Suitable examplesinclude the Fc fusion Enbrel® (etanercept) and the antibodies Humira®(adalimumab) and Remicade® (infliximab). Monoclonal antibodies (such asRemicade and Humira) engineered using the Fc variants of the presentinvention to increase FcFn binding, may translate to better efficacythrough an increased half-life.

In some embodiments, antibodies against infectious diseases are used.Antibodies against eukaryotic cells include antibodies targeting yeastcells, including but not limited to Saccharomyces cerevisiae, Hansenulapolymorpha, Kluyveromyces fragilis and K. lactis, Pichia guillerimondiiand P. pastoris, Schizosaccharomyces pombe, plasmodium falciparium, andYarrowia lipolytica.

Antibodies against additional fungal cells are also useful, includingtarget antigens associated with Candida strains including Candidaglabrata, Candida albicans, C. krusei, C. lusitaniae and C. maltosa, aswell as species of Aspergillus, Cryptococcus, Histoplasma, Coccidioides,Blastomyces, and Penicillium, among others

Antibodies directed against target antigens associated with protozoainclude, but are not limited to, antibodies associated with Trypanosoma,Leishmania species including Leishmania donovanii; Plasmodium spp.,Pneumocystis carinii, Cryptosporidium parvum, Giardia lamblia, Entamoebahistolytica, and Cyclospora cayetanensis.

Antibodies against prokaryotic antigens are also useful, includingantibodies against suitable bacteria such as pathogenic andnon-pathogenic prokaryotes including but not limited to Bacillus,including Bacillus anthracis; Vibrio, e.g. V. cholerae; Escherichia,e.g. Enterotoxigenic E. coli, Shigella, e.g. S. dysenteriae; Salmonella,e.g. S. typhi; Mycobacterium e.g. M. tuberculosis, M. leprae;Clostridium, e.g. C. botulinum, C. tetani, C. difficile, C.perfringens;Cornyebacterium, e.g. C. diphtheriae; Streptococcus, S. pyogenes, S.pneumoniae; Staphylococcus, e.g. S. aureus; Haemophilus, e.g. H.influenzae; Neisseria, e.g. N. meningitidis, N. gonorrhoeae; Yersinia,e.g. Y. lamblia, Y. pestis, Pseudomonas, e.g. P. aeruginosa, P. putida;Chlamydia, e.g. C. trachomatis; Bordetella, e.g. B. pertussis;Treponema, e.g. T palladium; B. anthracis, Y. pestis, Brucella spp., F.tularensis, B. mallei, B. pseudomallei, B. mallei, B. pseudomallei , C.botulinum, Salmonella spp., SEB V. cholerae toxin B, E. coli O157:H7,Listeria spp., Trichosporon beigelii, Rhodotorula species, Hansenulaanomala, Enterobacter sp., Klebsiella sp., Listeria sp., Mycoplasma sp.and the like.

In some aspects, the antibodies are directed against viral infections;these viruses include, but are not limited to, includingorthomyxoviruses, (e.g. influenza virus), paramyxoviruses (e.grespiratory syncytial virus, mumps virus, measles virus), adenoviruses,rhinoviruses, coronaviruses, reoviruses, togaviruses (e.g. rubellavirus), parvoviruses, poxviruses (e.g. variola virus, vaccinia virus),enteroviruses (e.g. poliovirus, coxsackievirus), hepatitis viruses(including A, B and C), herpesviruses (e.g. Herpes simplex virus,varicella-zoster virus, cytomegalovirus, Epstein-Barr virus),rotaviruses, Norwalk viruses, hantavirus, arenavirus, rhabdovirus (e.g.rabies virus), retroviruses (including HIV, HTLV-I and -II),papovaviruses (e.g. papillomavirus), polyomaviruses, and picornaviruses,and the like.

Optimized IgG Variant Properties

The present application also provides IgG variants that are optimizedfor a variety of therapeutically relevant properties. An IgG variantthat is engineered or predicted to display one or more optimizedproperties is herein referred to as an “optimized IgG variant”. The mostpreferred properties that may be optimized include but are not limitedto enhanced or reduced affinity for FcRn and increased or decreased invivo half-life. Suitable embodiments include antibodies that exhibitincreased binding affinity to FcRn at lowered pH, such as the pHassociated with endosomes, e.g. pH 6.0, while maintaining the reducedaffinity at higher pH, such as 7.4., to allow increased uptake intoendosomes but normal release rates. Similarly, these antibodies withmodulated FcRn binding may optionally have other desirable properties,such as modulated FcγR binding, such as outlined in U.S. Ser. Nos.11/174,287, 11/124,640, 10/822,231, 10/672,280, 10/379,392, and thepatent application entitled IgG Immunoglobulin variants with optimizedeffector function filed on Oct. 21, 2005 having application Ser. No.11/256,060. That is, optimized properties also include but are notlimited to enhanced or reduced affinity for an FcγR. In one optionalembodiment, the IgG variants are optimized to possess enhanced affinityfor a human activating FcγR, preferably FcγRIIIa in addition to the FcRnbinding profile. In yet another optional alternate embodiment, the IgGvariants are optimized to possess reduced affinity for the humaninhibitory receptor FcγRIIb. That is, particular embodiments embrace theuse of antibodies that show increased binding to FcRn, and increasedbinding to FcγRIIIa. Other embodiments utilize use of antibodies thatshow increased binding to FcRn, and increased binding to FcγRIIIa. Theseembodiments are anticipated to provide IgG polypeptides with enhancedtherapeutic properties in humans, for example enhanced effector functionand greater anti-cancer potency. In an alternate embodiment, the IgGvariants are optimized to have increased or reduced affinity for FcRnand increased or decreased affinity for a human FcγR, including but notlimited to FcγRI, FcγRIIa, FcγRIIb, FcγRIIc, FcγRIIIa, and FcγRIIIbincluding their allelic variations. These embodiments are anticipated toprovide IgG polypeptides with enhanced therapeutic properties in humans,for example increased serum half-life and reduced effector function. Inother embodiments, IgG variants provide enhanced affinity for FcRn andenhanced affinity for one or more FcγRs, yet reduced affinity for one ormore other FcγRs. For example, an IgG variant may have enhanced bindingto FcRn and FcγRIIIa, yet reduced binding to FcγRIIb. Alternately, anIgG variant may have reduced binding to FcRn and to FcγR's. In anotherembodiment, an IgG variant may have reduced affinity for FcRn andenhanced affinity for FcγRIIb, yet reduced affinity to one or moreactivating FcγRs. In yet another embodiment, an IgG variant may haveincreased serum half-life and reduced effector functions.

Preferred embodiments comprise optimization of binding to a human FcRnand FcγR, however in alternate embodiments the IgG variants possessenhanced or reduced affinity for FcRn and FcγR from nonhuman organisms,including but not limited to rodents and non-human primates. IgGvariants that are optimized for binding to a nonhuman FcRn may find usein experimentation. For example, mouse models are available for avariety of diseases that enable testing of properties such as efficacy,toxicity, and pharmacokinetics for a given drug candidate. As is knownin the art, cancer cells can be grafted or injected into mice to mimic ahuman cancer, a process referred to as xenografting. Testing of IgGvariants that comprise IgG variants that are optimized for FcRn mayprovide valuable information with regard to the clearancecharacteristics of the protein, its mechanism of clearance, and thelike. The IgG variants may also be optimized for enhanced functionalityand/or solution properties in aglycosylated form. The Fc ligands includebut are not limited to FcRn, FcγRs, C1q, and proteins A and G, and maybe from any source including but not limited to human, mouse, rat,rabbit, or monkey, preferably human. In an alternately preferredembodiment, the IgG variants are optimized to be more stable and/or moresoluble than the aglycosylated form of the parent IgG variant.

IgG variants can include modifications that modulate interaction with Fcligands other than FcRn and FcγRs, including but not limited tocomplement proteins, and Fc receptor homologs (FcRHs). FcRHs include butare not limited to FcRH1, FcRH2, FcRH3, FcRH4, FcRH5, and FcRH6 (Daviset al., 2002, Immunol. Reviews 190:123-136, entirely incorporated byreference).

Preferably, the Fc ligand specificity of the IgG variant will determineits therapeutic utility. The utility of a given IgG variant fortherapeutic purposes will depend on the epitope or form of the targetantigen and the disease or indication being treated. For most targetsand indications, enhanced FcRn binding may be preferable as the enhancedFcRn binding may result in an increase in serum half-life. Longer serumhalf-lives allow less frequent dosing or lower dosing of thetherapeutic. This is particularly preferable when the therapeutic agentis given in response to an indication that requires repeatedadministration. For some targets and indications, decreased FcRnaffinity may be preferable. This may be particularly preferable when avariant Fc with increased clearance or decreased serum half-life isdesired, for example in Fc polypeptides used as imaging agents orradio-therapeutics.

IgG variants may be used that comprise IgG variants that provideenhanced affinity for FcRn with enhanced activating FcγRs and/or reducedaffinity for inhibitory FcγRs. For some targets and indications, it maybe further beneficial to utilize IgG variants that provide differentialselectivity for different activating FcγRs; for example, in some casesenhanced binding to FcγRIIa and FcγRIIIa may be desired, but not FcγRI,whereas in other cases, enhanced binding only to FcγRIIa may bepreferred. For certain targets and indications, it may be preferable toutilize IgG variants that alter FcRn binding and enhance bothFcγR-mediated and complement-mediated effector functions, whereas forother cases it may be advantageous to utilize IgG variants that enhanceFcRn binding, or serum half-life, and either FcγR-mediated orcomplement-mediated effector functions. For some targets or cancerindications, it may be advantageous to reduce or ablate one or moreeffector functions, for example by knocking out binding to C1q, one ormore FcγR's, FcRn, or one or more other Fc ligands. For other targetsand indications, it may be preferable to utilize IgG variants thatprovide enhanced binding to the inhibitory FcγRIIb, yet VVT level,reduced, or ablated binding to activating FcγRs. This may beparticularly useful, for example, when the goal of an IgG variant is toinhibit inflammation or auto-immune disease, or modulate the immunesystem in some way. Because auto-immune diseases are generallylong-lasting and treatment is given in repeated dosing, their treatmentwith Fc variants with increased half-life from increased FcRn isparticularly preferred.

Modification may be made to improve the IgG stability, solubility,function, or clinical use. In a preferred embodiment, the IgG variantscan include modifications to reduce immunogenicity in humans. In a mostpreferred embodiment, the immunogenicity of an IgG variant is reducedusing a method described in U.S. Ser. No. 11/004,590, entirelyincorporated by reference. In alternate embodiments, the IgG variantsare humanized (Clark, 2000, Immunol Today 21:397-402, entirelyincorporated by reference).

The IgG variants can include modifications that reduce immunogenicity.Modifications to reduce immunogenicity can include modifications thatreduce binding of processed peptides derived from the parent sequence toMHC proteins. For example, amino acid modifications would be engineeredsuch that there are no or a minimal number of immune epitopes that arepredicted to bind, with high affinity, to any prevalent MHC alleles.Several methods of identifying MHC-binding epitopes in protein sequencesare known in the art and may be used to score epitopes in an IgGvariant. See for example WO 98/52976; WO 02/079232; WO 00/3317; U.S.Ser. Nos. 09/903,378; 10/039,170; U.S. Ser. No. 60/222,697; U.S. Ser.No. 10/754,296; PCT WO 01/21823; and PCT WO 02/00165; Mallios, 1999,Bioinformatics 15: 432-439; Mallios, 2001, Bioinformatics 17: 942-948;Sturniolo et al., 1999, Nature Biotech. 17: 555-561; WO 98/59244; WO02/069232; WO 02/77187; Marshall et al., 1995, J. Immunol. 154:5927-5933; and Hammer et al., 1994, J. Exp. Med. 180: 2353-2358, allentirely incorporated by reference. Sequence-based information can beused to determine a binding score for a given peptide—MHC interaction(see for example Mallios, 1999, Bioinformatics 15: 432-439; Mallios,2001, Bioinformatics 17: p942-948; Sturniolo et. al., 1999, NatureBiotech. 17: 555-561, all entirely incorporated by reference).

Engineering IgG Variants

Variants of the present invention may be designed by various means. Thevariants, as described herein, may be insertions, deletions,substitutions, other modifications, or combinations of these and otherchanges. A particularly novel embodiment of the present invention is thedesign of insertions and deletions that either improve or reduce thebinding of an Fc polypeptide to an Fc ligand. As disclosed herein,insertions or deletions may be made that increase or decrease theaffinity of the Fc polypeptide for FcRn. Insertions and deletions may bedesigned by rational approaches or by approaches that include the use orrandom components, such as random or semi-random library creation orscreening. In an alternative embodiment, substitutions are disclosedthat increase or decrease the affinity of the Fc polypeptide for FcRn.

Backbone Modifications: Insertions and Deletions

Variant Fc polypeptides may be created by substituting a variant aminoacid in place of the parent amino acid at a position in the Fcpolypeptide. By substituting one or more amino acids for variant aminoacids in the Fc polypeptide, the side chains at those positions arealtered. Most useful substitutions modify the Fc properties by alteringthe Fc side chains. The substituted side chains may interact directly orindirectly with an Fc binding partner that is associated with an Fcfunction or property. The at least one substitution alters the covalentstructure of one or more side chains of the parent Fc polypeptide.

Alternatively, variant Fc polypeptides may be created that change thecovalent structure of the backbone of the parent Fc polypeptide. Thebackbone atoms in proteins are the peptide nitrogen, the alpha carbon,the carbonyl or peptide carbon and the carbonyl oxygen. Changing thecovalent structure of the backbone provides additional methods ofaltering the properties of the Fc polypeptides. The covalent structureof the Fc backbone may be altered by the addition of atoms into thebackbone, e.g. by inserting one or more amino acids, or the subtractionof atoms from the backbone, e.g. by deleting one or more amino acids.The covalent structure of the backbone may also be altered by changingindividual atoms of the backbone to other atoms (Deechongkit et al., JAm Chem Soc. 2004. 126(51):16762-71, entirely incorporated byreference). As is known in the art and is illustrated herein, insertionsor deletions of amino acids in Fc polypeptides may be done by insertingor deleting the corresponding nucleotides in the DNA encoding the Fcpolypeptide. Alternatively, as is known in the art, insertions ordeletions of amino acids may be done during synthesis of Fcpolypeptides.

The design of insertions or deletions of amino acids that alter theinteraction of the Fc polypeptide with one or more binding partners(e.g. FcgammaR's, FcRn, C1q) may be done by considering the structure ofthe complex of the Fc polypeptide and its binding partner. In a lesspreferred embodiment, the design may be done by considering thestructure of the Fc polypeptide and information about the Fc regioninvolved in binding the binding partner. This information may beobtained by mutagenesis experiments, phage display experiments, homologycomparisons, computer modeling or other means.

Preferred positions in the amino acid sequence for insertions ordeletions that affect the Fc binding interactions, but do not affect theoverall structure, stability, expression or use of the Fc polypeptide,are in loops that are involved in the Fc/Fc-binding partnerinteractions. To alter FcRn binding to the Fc polypeptide, positions244-257, 279-284, 307-317, 383-390, and 428-435 are preferred looplocations for insertions or deletions (numbering from EU index of Kabatet al., Burmeister et al., 1994, Nature, 372:379-383; Martin et al.,2001, Mol Cell 7:867-877, all entirely incorporated by reference). Toalter the Fcgamma receptor binding to the Fc polypeptide, positions229-239, 266-273, 294-299, and 324-331 are preferred loop locations forinsertions or deletions (numbering from EU index of Kabat et al., PDBcode 1 E4K.pdb Sondermann et al. Nature. 2000 406:267, all entirelyincorporated by reference). Loops are regions of the polypeptide notinvolved in alpha helical or beta sheet structure. Loops positions arepositions that are not in either alpha helical or beta sheet structures(van Holde, Johnson and Ho. Principles of Physical Biochemistry.Prentice Hall, New Jersey 1998, Chapter 1 pp2-67, entirely incorporatedby reference). Loop positions are preferred because the backbone atomsare typically more flexible and less likely involved in hydrogen bondscompared to the backbone atoms of alpha helices and beta sheets.Therefore, the lengthening or shortening of a loop due to an insertionor deletion of one or more amino acids is less likely to lead to large,disruptive changes to the Fc polypeptide, including stability,expression or other problems.

Insertions and deletions may be used to alter the length of thepolypeptide. For example, in loop regions, altering the loop lengthresults in altered flexibility and conformational entropy of the loop.Insertions in a loop will generally increase the conformational entropyof the loop, which may be defined as Boltzman's constant multiplied bythe natural logarithm of the number of possible conformations (vanHolde, Johnson and Ho. Principles of Physical Biochemistry. PrenticeHall, New Jersey 1998, pp 78, entirely incorporated by reference). Byinserting at least one amino acid into a polypeptide, the total numberof conformations available to the polypeptide increases. Theseadditional conformations may be beneficial for forming favorableFc/Fc-binding partner interactions because the Fc polypeptide may useone of the additional conformations in binding the Fc-binding protein.In this case, the insertion may lead to stronger Fc/Fc-binding partnerinteractions. If the additional conformations are not used in thebinding interface, then the insertion may lead to weaker Fc/Fc-bindingpartner interactions, because the additional conformations would competewith the binding-competent conformation. Similarly, deletion of apolypeptide segment may also lead to either stronger or weaker Fc/Fcbinding-partner interactions. If deletion of a segment, which reducesthe possible number of backbone conformations, removes thebinding-competent conformation, then the deletion may lead to weakerFc/Fc-binding partner interactions. If the deletion does not remove thebinding-competent conformation, then the deletion may lead to strongerFc/Fc-binding partner interactions because the deletion may removeconformations that compete with the binding-competent conformation.

Insertions and deletions may be used to alter the positions andorientations of the amino acids in the Fc polypeptide. Becauseinsertions and deletions cause a change in the covalent structure of thebackbone, they necessarily cause a change in the positions of thebackbone atoms. FIG. 7 compares the backbone positions at some loopsegments, marked L1 to L4, in three different backbones. The referencebackbone structure contains four loop segments, whereas the deletionbackbone lacks segment L1 and the insertion segment comprises anadditional segment before, ie, N-terminal to, segment L1. Deletions andinsertions cause the largest change in the backbone structure near thesite of the insertion or deletion. By deleting a segment near theN-terminal end of the loop, e.g. segment L1, the loop shortens and theremaining segments shift their position closer to the loop N-terminus.This has the effect of moving the L2 segment toward the prior locationof the L1 segment and toward the loop N-terminus. This change inposition of the L2 segment toward the L1 segment may strengthen thebinding of the Fc/Fc-binding partner complex and is preferred when thereis prior information suggesting that the amino acid or amino acidslocated in L2 make favorable interactions with the Fc-binding partner,when located in L1. For example, if L2 contains alanine and tyrosine andsubstitution of two L1 amino acids for alanine and tyrosine previouslylead to an Fc variant with increased binding, then deletion of L1 maycreate an Fc variant with increased affinity for the Fc-binding partner.

Similarly, an insertion of a polypeptide segment into an Fc polypeptideat the N-terminal side of a loop causes the positions of the loopsegments to be shifted toward the C-terminal side of the loop. In FIG.7, an insertion of one or more amino acids before, i.e. N-terminally to,segment L1 alters the backbone conformation including a shift of the L1segment toward the C-terminal end of the loop. This type of insertion ispreferred when the amino acids located in segment L1 are known to makefavorable interactions when located in the L2 positions, as theinsertion may lead to stronger Fc/Fc-binding partner interactions. Ifweaker Fc/Fc-binding partner interactions are desired, then theinsertion may be used to shift unfavorable amino acid into a newposition. The inserted, deleted and reference segments (L1 to L4 in FIG.7) may be one or more than one amino acid in the Fc polypeptide.

Alternatively, insertions or deletions may be used at the C-terminal endof loops in a manner analogous to the insertions or deletions at theN-terminal end of loops. Insertions at the loop C-terminus may lead to amovement of the positions N-terminal of the insertion toward the loopN-terminus. Deletions at the loop C-terminus may lead to a movement ofthe positions N-terminal of the deletion toward the loop C-terminus. Thechoice of using an insertion or deletion at the N-terminal or C-terminalend of the loop is based on the amino acids located in the loop, thedesire for increased or decreased Fc/Fc-binding partner affinity, andthe positional shift desired.

Insertions or deletions may be used in any region of an Fc polypeptide,including the loops, the alpha helical, and the beta sheet regions.Preferred locations for insertions and deletions include loop regions,which are those that are not alpha helical or beta sheet regions. Loopsare preferred because they generally accept alterations in the backbonebetter than alpha helixes or beta sheets. The particularly preferredlocations for insertions or deletions that result in strongerprotein/protein interactions are at the N-terminal or C-terminal edgesof a loop. If the loop side chains are involve in the Fc/Fc-bindingpartner interactions, then insertions or deletion at the edges are lesslikely to lead to strongly detrimental changes in the bindinginteractions. Deletions within the exact center of the loop are morelikely to remove important residues in the Fc/Fc-binding partnerinterface and insertions within the exact center of the loop are morelikely to create unfavorable interactions in the Fc/Fc-binding partnerinterface. The number of residues deleted or inserted may be determinedby the size of the backbone change desired with insertions or deletionsof 15 or less residues being preferred, insertions or deletions of 10 orless residues being more preferred, and insertions or deletions of 5 orless residues being most preferred.

Once the position and size of an Fc deletion variant is designed, theentire polypeptide sequence is completely determined and the polypeptidemay be constructed by methods known in the art.

Fc insertion variants, however, have the additional step of designingthe sequence of the at least one amino acid to be inserted. Insertionsof polar residues, including Ser, Thr, Asn, Gln, Ala, Gly, His, arepreferred at positions expected to be exposed in the Fc polypeptide. Thesmaller amino acids, including Ser, Thr, and Ala, are particularlypreferred as the small size is less likely to sterically interfere withthe Fc/Fc-binding partner interactions. Ser and Thr also have thecapability to hydrogen bond with atoms on the Fc-binding partner.

Insertions also have the added flexibility that the inserted polypeptidemay be designed to make favorable interactions with the Fc-bindingpartner as would be desire when stronger Fc/Fc-binding partner bindingis desired. The length of the backbone insertion may be determined bymodeling the variant backbone with a simple, generic sequence to beinserted. For example, polyserine, polyglycine or polyalanine insertionsof different lengths may be constructed and modeled. Modeling may bedone by a variety of methods, including homology modeling based on knownthree-dimensional structures of homologues comprising the insertion, andby computer modeling including MODELLER (M. A. Marti-Renom et al. Annu.Rev. Biophys. Biomol. Struct. 29, 291-325, 2000) and ROSETTA (Kuhlman etal. (2003). Science 302, 1364-8), both entirely incorporated byreference. Typically, various backbone conformations are initiallygenerated and the final backbone structure may be determined after theidentities of the side chain are established. The side chains may bedesigned by FDA® algorithms (U.S. Pat. Nos. 6,188,965; 6,269,312;6,403,312; 6,801,861; 6,804,611; 6,792,356, 6,950,754, and U.S. Ser.Nos. 09/782,004; 09/927,790; 10/101,499; 10/666,307; 10/666311;10/218,102, all entirely incorporated by reference).

Insertions and deletions may be made to alter the binding of Fcpolypeptides to FcgammaR in an analogous manner to the described methodto alter FcRn-binding properties. Fc domains bind to the FcgammaR at theposition indicated in FIG. 1. Structures of the Fc/FcgammaR complex,including PDB codes 1T89 and 1IIS (Radaev S et al. J. Biol. Chem. v276,p.16469-16477 entirely incorporated by reference), demonstrate theinteracting residues and loops between the two structures. Mutagenesisresults such as those found in U.S. Ser. No. 11/124620 and U.S. Pat. No.6,737,056, both entirely incorporated by reference) all have utility indetermined appropriate shifts of backbone positioning.

Insertions and deletions may be designed in any polypeptide besides Fcpolypeptides by the methods described herein. For example, insertions ordeletions in the TNF superfamily member, APRIL, may be designed with theaid of its three-dimensional structure (PDB code 1XU1.pdb, Hymowitz, etal. (2005) J. Biol. Chem. 280:7218, entirely incorporated by reference).Insertions or deletions may be designed to increase APRIL binding to itsreceptor, TACI. The loop residues preferred as insertion or deletionsites are residues Ser118-Va1124, Asp164-Phe167, Pro192-Ala198,Pro221-Lys226. These loops interact with TACI in the APRIL/TACI complexand mediate binding.

Polypeptides Incorporating Variants

The IgG variants can be based on human IgG sequences, and thus human IgGsequences are used as the “base” sequences against which other sequencesare compared, including but not limited to sequences from otherorganisms, for example rodent and primate sequences. IgG variants mayalso comprise sequences from other immunoglobulin classes such as IgA,IgE, IgD, IgM, and the like. It is contemplated that, although the IgGvariants are engineered in the context of one parent IgG, the variantsmay be engineered in or “transferred” to the context of another, secondparent IgG. This is done by determining the “equivalent” or“corresponding” residues and substitutions between the first and secondIgG, typically based on sequence or structural homology between thesequences of the IgGs. In order to establish homology, the amino acidsequence of a first IgG outlined herein is directly compared to thesequence of a second IgG. After aligning the sequences, using one ormore of the homology alignment programs known in the art (for exampleusing conserved residues as between species), allowing for necessaryinsertions and deletions in order to maintain alignment (i.e., avoidingthe elimination of conserved residues through arbitrary deletion andinsertion), the residues equivalent to particular amino acids in theprimary sequence of the first IgG variant are defined. Alignment ofconserved residues preferably should conserve 100% of such residues.However, alignment of greater than 75% or as little as 50% of conservedresidues is also adequate to define equivalent residues. Equivalentresidues may also be defined by determining structural homology betweena first and second IgG that is at the level of tertiary structure forIgGs whose structures have been determined. In this case, equivalentresidues are defined as those for which the atomic coordinates of two ormore of the main chain atoms of a particular amino acid residue of theparent or precursor (N on N, CA on CA, C on C and O on O) are within0.13 nm and preferably 0.1 nm after alignment. Alignment is achievedafter the best model has been oriented and positioned to give themaximum overlap of atomic coordinates of non-hydrogen protein atoms ofthe proteins. Regardless of how equivalent or corresponding residues aredetermined, and regardless of the identity of the parent IgG in whichthe IgGs are made, what is meant to be conveyed is that the IgG variantsdiscovered by can be engineered into any second parent IgG that hassignificant sequence or structural homology with the IgG variant. Thusfor example, if a variant antibody is generated wherein the parentantibody is human IgG1, by using the methods described above or othermethods for determining equivalent residues, the variant antibody may beengineered in another IgG1 parent antibody that binds a differentantigen, a human IgG2 parent antibody, a human IgA parent antibody, amouse IgG2a or IgG2b parent antibody, and the like. Again, as describedabove, the context of the parent IgG variant does not affect the abilityto transfer the IgG variants to other parent IgGs.

Methods for engineering, producing, and screening IgG variants areprovided. The described methods are not meant to constrain to anyparticular application or theory of operation. Rather, the providedmethods are meant to illustrate generally that one or more IgG variantsmay be engineered, produced, and screened experimentally to obtain IgGvariants with optimized effector function. A variety of methods aredescribed for designing, producing, and testing antibody and proteinvariants in U.S. Ser. No. 10/754,296, and U.S. Ser. No. 10/672,280, bothentirely incorporated by reference.

A variety of protein engineering methods may be used to design IgGvariants with optimized effector function. In one embodiment, astructure-based engineering method may be used, wherein availablestructural information is used to guide substitutions, insertions ordeletions. In a preferred embodiment, a computational screening methodmay be used, wherein substitutions are designed based on their energeticfitness in computational calculations. See for example U.S. Ser. No.10/754,296 and U.S. Ser. No. 10/672,280, and references cited therein,all entirely incorporated by reference.

An alignment of sequences may be used to guide substitutions at theidentified positions. One skilled in the art will appreciate that theuse of sequence information may curb the introduction of substitutionsthat are potentially deleterious to protein structure. The source of thesequences may vary widely, and include one or more of the knowndatabases, including but not limited to the Kabat database (NorthwesternUniversity); Johnson & Wu, 2001, Nucleic Acids Res. 29:205-206; Johnson& Wu, 2000, Nucleic Acids Res. 28:214-218), the IMGT database (IMGT, theinternational ImMunoGeneTics information system®; Lefranc et al., 1999,Nucleic Acids Res. 27:209-212; Ruiz et al., 2000 Nucleic Acids Res.28:219-221; Lefranc et al., 2001, Nucleic Acids Res. 29:207-209; Lefrancet al., 2003, Nucleic Acids Res. 31:307-310), and VBASE, all entirelyincorporated by reference. Antibody sequence information can beobtained, compiled, and/or generated from sequence alignments ofgermline sequences or sequences of naturally occurring antibodies fromany organism, including but not limited to mammals. One skilled in theart will appreciate that the use of sequences that are human orsubstantially human may further have the advantage of being lessimmunogenic when administered to a human. Other databases which are moregeneral nucleic acid or protein databases, i.e. not particular toantibodies, include but are not limited to SwissProt, GenBank Entrez,and EMBL Nucleotide Sequence Database. Aligned sequences can include VH,VL, CH, and/or CL sequences. There are numerous sequence-based alignmentprograms and methods known in the art, and all of these find use in thegeneration of sequence alignments.

Alternatively, random or semi-random mutagenesis methods may be used tomake amino acid modifications at the desired positions. In these casespositions are chosen randomly, or amino acid changes are made usingsimplistic rules. For example all residues may be mutated to alanine,referred to as alanine scanning. Such methods may be coupled with moresophisticated engineering approaches that employ selection methods toscreen higher levels of sequence diversity. As is well known in the art,there are a variety of selection technologies that may be used for suchapproaches, including, for example, display technologies such as phagedisplay, ribosome display, cell surface display, and the like, asdescribed below.

Methods for production and screening of IgG variants are well known inthe art. General methods for antibody molecular biology, expression,purification, and screening are described in Antibody Engineering,edited by Duebel & Kontermann, Springer-Verlag, Heidelberg, 2001; andHayhurst & Georgiou, 2001, Curr Opin Chem Biol 5:683-689; Maynard &Georgiou, 2000, Annu Rev Biomed Eng 2:339-76. Also see the methodsdescribed in U.S. Ser. Nos. 10/754,296; 10/672,280; and 10/822,231; and11/124,620, all entirely incorporated by reference. Preferred variantsof the present invention include those found in FIGS. 8a -8 b.Alternatively preferred variants of the present invention include thosefound in FIGS. 9a -9 b. Additionally alternatively preferred variants ofthe present invention include those found in FIGS. 10a -10 b. Thesevariants have shown increased binding to the Fc receptor, FcRn, asillustrated in the examples.

Making IgG Variants

The IgG variants can be made by any method known in the art. In oneembodiment, the IgG variant sequences are used to create nucleic acidsthat encode the member sequences, and that may then be cloned into hostcells, expressed and assayed, if desired. These practices are carriedout using well-known procedures, and a variety of methods that may finduse in are described in Molecular Cloning—A Laboratory Manual, 3^(rd)Ed. (Maniatis, Cold Spring Harbor Laboratory Press, New York, 2001), andCurrent Protocols in Molecular Biology (John Wiley & Sons), bothentirely incorporated by reference. The nucleic acids that encode theIgG variants may be incorporated into an expression vector in order toexpress the protein. Expression vectors typically include a proteinoperably linked, that is, placed in a functional relationship, withcontrol or regulatory sequences, selectable markers, any fusionpartners, and/or additional elements. The IgG variants may be producedby culturing a host cell transformed with nucleic acid, preferably anexpression vector, containing nucleic acid encoding the IgG variants,under the appropriate conditions to induce or cause expression of theprotein. A wide variety of appropriate host cells may be used, includingbut not limited to mammalian cells, bacteria, insect cells, and yeast.For example, a variety of cell lines that may find use are described inthe ATCC cell line catalog, available from the American Type CultureCollection, entirely incorporated by reference. The methods ofintroducing exogenous nucleic acid into host cells are well known in theart, and will vary with the host cell used.

In a preferred embodiment, IgG variants are purified or isolated afterexpression. Antibodies may be isolated or purified in a variety of waysknown to those skilled in the art. Standard purification methods includechromatographic techniques, electrophoretic, immunological,precipitation, dialysis, filtration, concentration, and chromatofocusingtechniques. As is well known in the art, a variety of natural proteinsbind antibodies, for example bacterial proteins A, G, and L, and theseproteins may find use in purification. Often, purification may beenabled by a particular fusion partner. For example, proteins may bepurified using glutathione resin if a GST fusion is employed, Ni⁺²affinity chromatography if a His-tag is employed, or immobilizedanti-flag antibody if a flag-tag is used. For general guidance insuitable purification techniques, see Antibody Purification: Principlesand Practice, 3^(rd) Ed., Scopes, Springer-Verlag, NY, 1994, entirelyincorporated by reference.

Screening IgG Variants

Fc variants may be screened using a variety of methods, including butnot limited to those that use in vitro assays, in vivo and cell-basedassays, and selection technologies. Automation and high-throughputscreening technologies may be utilized in the screening procedures.Screening may employ the use of a fusion partner or label, for examplean immune label, isotopic label, or small molecule label such as afluorescent or colorimetric dye.

In a preferred embodiment, the functional and/or biophysical propertiesof Fc variants are screened in an in vitro assay. In a preferredembodiment, the protein is screened for functionality, for example itsability to catalyze a reaction or its binding affinity to its target.

As is known in the art, subsets of screening methods are those thatselect for favorable members of a library. The methods are hereinreferred to as “selection methods”, and these methods find use in thepresent invention for screening Fc variants. When protein libraries arescreened using a selection method, only those members of a library thatare favorable, that is which meet some selection criteria, arepropagated, isolated, and/or observed. A variety of selection methodsare known in the art that may find use in the present invention forscreening protein libraries. Other selection methods that may find usein the present invention include methods that do not rely on display,such as in vivo methods. A subset of selection methods referred to as“directed evolution” methods are those that include the mating orbreading of favorable sequences during selection, sometimes with theincorporation of new mutations.

In a preferred embodiment, Fc variants are screened using one or morecell-based or in vivo assays. For such assays, purified or unpurifiedproteins are typically added exogenously such that cells are exposed toindividual variants or pools of variants belonging to a library. Theseassays are typically, but not always, based on the function of the Fcpolypeptide; that is, the ability of the Fc polypeptide to bind to itstarget and mediate some biochemical event, for example effectorfunction, ligand/receptor binding inhibition, apoptosis, and the like.Such assays often involve monitoring the response of cells to the IgG,for example cell survival, cell death, change in cellular morphology, ortranscriptional activation such as cellular expression of a natural geneor reporter gene. For example, such assays may measure the ability of Fcvariants to elicit ADCC, ADCP, or CDC. For some assays additional cellsor components, that is in addition to the target cells, may need to beadded, for example example serum complement, or effector cells such asperipheral blood monocytes (PBMCs), NK cells, macrophages, and the like.Such additional cells may be from any organism, preferably humans, mice,rat, rabbit, and monkey. Antibodies may cause apoptosis of certain celllines expressing the target, or they may mediate attack on target cellsby immune cells which have been added to the assay. Methods formonitoring cell death or viability are known in the art, and include theuse of dyes, immunochemical, cytochemical, and radioactive reagents.Transcriptional activation may also serve as a method for assayingfunction in cell-based assays. Alternatively, cell-based screens areperformed using cells that have been transformed or transfected withnucleic acids encoding the variants. That is, Fc variants are not addedexogenously to the cells.

The biological properties of the IgG variants may be characterized incell, tissue, and whole organism experiments. As is known in the art,drugs are often tested in animals, including but not limited to mice,rats, rabbits, dogs, cats, pigs, and monkeys, in order to measure adrug's efficacy for treatment against a disease or disease model, or tomeasure a drug's pharmacokinetics, toxicity, and other properties. Theanimals may be referred to as disease models. Therapeutics are oftentested in mice, including but not limited to nude mice, SCID mice,xenograft mice, and transgenic mice (including knockins and knockouts).Such experimentation may provide meaningful data for determination ofthe potential of the protein to be used as a therapeutic. Any organism,preferably mammals, may be used for testing. For example because oftheir genetic similarity to humans, monkeys can be suitable therapeuticmodels, and thus may be used to test the efficacy, toxicity,pharmacokinetics, or other property of the IgGs. Tests of the in humansare ultimately required for approval as drugs, and thus of course theseexperiments are contemplated. Thus the IgGs may be tested in humans todetermine their therapeutic efficacy, toxicity, immunogenicity,pharmacokinetics, and/or other clinical properties.

Methods of Using IgG Variants

The IgG variants may find use in a wide range of products. In oneembodiment the IgG variant is a therapeutic, a diagnostic, or a researchreagent, preferably a therapeutic. The IgG variant may find use in anantibody composition that is monoclonal or polyclonal. In a preferredembodiment, the IgG variants are used to kill target cells that bear thetarget antigen, for example cancer cells. In an alternate embodiment,the IgG variants are used to block, antagonize or agonize the targetantigen, for example for antagonizing a cytokine or cytokine receptor.In an alternately preferred embodiment, the IgG variants are used toblock, antagonize or agonize the target antigen and kill the targetcells that bear the target antigen.

The IgG variants may be used for various therapeutic purposes. In apreferred embodiment, an antibody comprising the IgG variant isadministered to a patient to treat an antibody-related disorder. A“patient” for the purposes includes humans and other animals, preferablymammals and most preferably humans. By “antibody related disorder” or“antibody responsive disorder” or “condition” or “disease” herein aremeant a disorder that may be ameliorated by the administration of apharmaceutical composition comprising an IgG variant. Antibody relateddisorders include but are not limited to autoimmune diseases,immunological diseases, infectious diseases, inflammatory diseases,neurological diseases, and oncological and neoplastic diseases includingcancer. By “cancer” and “cancerous” herein refer to or describe thephysiological condition in mammals that is typically characterized byunregulated cell growth. Examples of cancer include but are not limitedto carcinoma, lymphoma, blastoma, sarcoma (including liposarcoma),neuroendocrine tumors, mesothelioma, schwanoma, meningioma,adenocarcinoma, melanoma, and leukemia and lymphoid malignancies.

In one embodiment, an IgG variant is the only therapeutically activeagent administered to a patient. Alternatively, the IgG variant isadministered in combination with one or more other therapeutic agents,including but not limited to cytotoxic agents, chemotherapeutic agents,cytokines, growth inhibitory agents, anti-hormonal agents, kinaseinhibitors, anti-angiogenic agents, cardioprotectants, or othertherapeutic agents. The IgG varariants may be administered concomitantlywith one or more other therapeutic regimens. For example, an IgG variantmay be administered to the patient along with chemotherapy, radiationtherapy, or both chemotherapy and radiation therapy. In one embodiment,the IgG variant may be administered in conjunction with one or moreantibodies, which may or may not be an IgG variant. In accordance withanother embodiment, the IgG variant and one or more other anti-cancertherapies are employed to treat cancer cells ex vivo. It is contemplatedthat such ex vivo treatment may be useful in bone marrow transplantationand particularly, autologous bone marrow transplantation. It is ofcourse contemplated that the IgG variants can be employed in combinationwith still other therapeutic techniques such as surgery.

A variety of other therapeutic agents may find use for administrationwith the IgG variants. In one embodiment, the IgG is administered withan anti-angiogenic agent. By “anti-angiogenic agent” as used herein ismeant a compound that blocks, or interferes to some degree, thedevelopment of blood vessels. The anti-angiogenic factor may, forinstance, be a small molecule or a protein, for example an antibody, Fcfusion, or cytokine, that binds to a growth factor or growth factorreceptor involved in promoting angiogenesis. The preferredanti-angiogenic factor herein is an antibody that binds to VascularEndothelial Growth Factor (VEGF). In an alternate embodiment, the IgG isadministered with a therapeutic agent that induces or enhances adaptiveimmune response, for example an antibody that targets CTLA-4. In analternate embodiment, the IgG is administered with a tyrosine kinaseinhibitor. By “tyrosine kinase inhibitor” as used herein is meant amolecule that inhibits to some extent tyrosine kinase activity of atyrosine kinase. In an alternate embodiment, the IgG variants areadministered with a cytokine.

Pharmaceutical compositions are contemplated wherein an IgG variant andone or more therapeutically active agents are formulated. Formulationsof the IgG variants are prepared for storage by mixing the IgG havingthe desired degree of purity with optional pharmaceutically acceptablecarriers, excipients or stabilizers (Remington's Pharmaceutical Sciences16th edition, Osol, A. Ed., 1980, entirely incorporated by reference),in the form of lyophilized formulations or aqueous solutions. Theformulations to be used for in vivo administration are preferablysterile. This is readily accomplished by filtration through sterilefiltration membranes or other methods. The IgG variants and othertherapeutically active agents disclosed herein may also be formulated asimmunoliposomes, and/or entrapped in microcapsules.

The concentration of the therapeutically active IgG variant in theformulation may vary from about 0.1 to 100% by weight. In a preferredembodiment, the concentration of the IgG is in the range of 0.003 to 1.0molar. In order to treat a patient, a therapeutically effective dose ofthe IgG variant may be administered. By “therapeutically effective dose”herein is meant a dose that produces the effects for which it isadministered. The exact dose will depend on the purpose of thetreatment, and will be ascertainable by one skilled in the art usingknown techniques. Dosages may range from 0.01 to 100 mg/kg of bodyweight or greater, for example 0.01, 0.1, 1.0, 10, or 50 mg/kg of bodyweight, with 1 to 10mg/kg being preferred. As is known in the art,adjustments for protein degradation, systemic versus localized delivery,and rate of new protease synthesis, as well as the age, body weight,general health, sex, diet, time of administration, drug interaction andthe severity of the condition may be necessary, and will beascertainable with routine experimentation by those skilled in the art.

Administration of the pharmaceutical composition comprising an IgGvariant, preferably in the form of a sterile aqueous solution, may bedone in a variety of ways, including, but not limited to, orally,subcutaneously, intravenously, parenterally, intranasally,intraotically, intraocularly, rectally, vaginally, transdermally,topically (e.g., gels, salves, lotions, creams, etc.),intraperitoneally, intramuscularly, intrapulmonary (e.g., AERx®inhalable technology commercially available from Aradigm, or Inhance®pulmonary delivery system commercially available from NektarTherapeutics, etc.). Therapeutic described herein may be administeredwith other therapeutics concomitantly, i.e., the therapeutics describedherein may be co-administered with other therapies or therapeutics,including for example, small molecules, other biologicals, radiationtherapy, surgery, etc.

EXAMPLES

Examples are provided below to illustrate the present invention. Theseexamples are not meant to constrain the present invention to anyparticular application or theory of operation. For all positionsdiscussed in the present invention, numbering is according to the EUindex as in Kabat (Kabat et al., 1991, Sequences of Proteins ofImmunological Interest, 5th Ed., United States Public Health Service,National Institutes of Health, Bethesda, entirely incorporated byreference). Those skilled in the art of antibodies will appreciate thatthis convention consists of nonsequential numbering in specific regionsof an immunoglobulin sequence, enabling a normalized reference toconserved positions in immunoglobulin families. Accordingly, thepositions of any given immunoglobulin as defined by the EU index willnot necessarily correspond to its sequential sequence.

Example 1: DNA Construction, Expression, and Purification of Fc Variants

Fc variants were constructed using the human IgG1 Fc domain and thevariable domain of trastuzumab (Herceptin®, Genentech). The Fcpolypeptides were part of Alemtuzumab, An anti-HER2 antibody or AC10.Alemtuzumab (Campath®, a registered trademark of Millenium) is ahumanized monoclonal antibody currently approved for treatment of B-cellchronic lymphocytic leukemia (Hale et al., 1990, Tissue Antigens35:118-127, entirely incorporated by reference). Trastuzumab(Herceptin®, a registered trademark of Genentech) is an anti-HER2/neuantibody for treatment of metastatic breast cancer. The heavy and lightchain sequences of the anti-HER2 antibody are shown in FIG. 22. AC10 isan anti-CD30 monoclonal antibody. The Herceptin variable region wasassembled using recursive PCR. This variable region was then cloned withhuman IgG1 into the pcDNA3.1/Zeo(+) vector (Invitrogen), shown in FIG.11. Plasmids were propagated in One Shot TOP10 E. coli cells(Invitrogen) and purified using the Hi-Speed Plasmid Maxi Kit (Qiagen).Plasmids were sequenced to verify the presence of the cloned inserts.

Site-directed mutagenesis was done using the Quikchange™ method(Stratagene). Plasmids containing the desired substitutions, insertions,and deletions were propagated in One Shot TOP10 E. coli cells(Invitrogen) and purified using the Hi-Speed Plasmid Maxi Kit (Qiagen).DNA was sequenced to confirm the fidelity of the sequences.

Plasmids containing heavy chain gene (VH-Cγ1-Cγ2-Cγ3) (wild-type orvariants) were co-transfected with plasmid containing light chain gene(VL-Cη) into 293T cells. Media were harvested 5 days after transfection,and antibodies were purified from the supernatant using protein Aaffinity chromatography (Pierce). Protein A binding characteristics ofsome modified Fc's are shown in FIG. 26. Antibody concentrations weredetermined by bicinchoninic acid (BCA) assay (Pierce).

Example 2: Binding Affinity Measurements

Binding of Fc polypeptides to Fc ligands was assayed with surfaceplasmon resonance measurements. Surface plasmon resonance (SPR)measurements were performed using a BIAcore 3000 instrument (BlAcoreAB). Wild-type or variant antibody was captured using immobilizedprotein L (Pierce Biotechnology, Rockford, Ill.), and binding toreceptor analyte was measured. Protein L was covalently coupled to a CM5sensor chip at a concentration of 1 uM in 10 mM sodium acetate, pH 4.5on a CM5 sensor chip usingN-hydroxysuccinimide/N-ethyl-N′-(-3-dimethylamino-propyl) carbodiimide(NHS/EDC) at a flow rate of 5 ul/min. Flow cell 1 of every sensor chipwas mocked with NHS/EDC as a negative control of binding. Running bufferwas 0.01 M HEPES pH 7.4, 0.15 M NaCl, 3 mM EDTA, 0.005% v/v SurfactantP20 (HBS-EP, Biacore, Uppsala, Sweden), and chip regeneration buffer was10 mM glycine-HCl pH 1.5. 125 nM Wild-type or variant anti-HER2 antibodywas bound to the protein L CM5 chip in HBS-EP at 1 ul/min for 5 minutes.FcRn-His-GST analyte, a FcRn fused to a His-tag and glutathione Stransferase, in serial dilutions between 1 and 250 nM, were injected for20 minutes association, 10 minutes dissociation, in HBS-EP at 10 ul/min.Response, measured in resonance units (RU), was acquired at 1200 secondsafter receptor injection, reflecting near steady state binding. A cyclewith antibody and buffer only provided baseline response. RU versus1/log concentration plots were generated and fit to a sigmoidal doseresponse using nonlinear regression with GraphPad Prism.

Binding of Fc polypeptides to Fc ligands was also done with AlphaScreen™(Amplified Luminescent Proximity Homogeneous Assay). AlphaScreen™ is abead-based non-radioactive luminescent proximity assay. Laser excitationof a donor bead excites oxygen, which if sufficiently close to theacceptor bead will generate a cascade of chemiluminescent events,ultimately leading to fluorescence emission at 520-620 nm. The principaladvantage of the AlphaScreen™ is its sensitivity. Because one donor beademits up to 60,000 excited oxygen molecules per second, signalamplification is extremely high, allowing detection down to attomolar(10⁻¹⁸) levels. Wild-type antibody was biotinylated by standard methodsfor attachment to streptavidin donor beads, and tagged Fc ligand, forexample FcRn, FcgammaR or Protein A, was bound to glutathione chelateacceptor beads. The AlphaScreen™ was applied as a direct binding assayin which the Fc/Fc ligand interactions bring together the donor andacceptor beads to create the measured signal. Addtionally, theAlphaScreen™ was applied as a competition assay for screening designedFc polypeptides. In the absence of competing Fc polypeptides, wild-typeantibody and FcRn interact and produce a signal at 520-620 nm. UntaggedFc domains compete with wild-type Fc/FcRn interaction, reducingfluorescence quantitatively to enable determination of relative bindingaffinities.

Example 3: FcRn-Binding Properties of Fc Variants

Binding affinity of IgG1 Fc to FcRn was measured with variant antibodiesusing AlphaScreen™. The Fc polypeptides were part of Alemtuzumab orTrastuzumab. Alemtuzumab (Campath®, Ilex) is a humanized monoclonalantibody currently approved for treatment of B-cell chronic lymphocyticleukemia (Hale et al., 1990, Tissue Antigens 35:118-127, entirelyincorporated by reference). Trastuzumab (Herceptin®, Genentech) is ananti-HER2/neu antibody for treatment of metastatic breast cancer.

Competitive AlphaScreen™ data were collected to measure the relativebinding of the Fc variants compared to the wild-type antibody in 0.1 Msodium phosphate pH6.0 with 25 mM sodium chloride. Examples of theAlphaScreen™ signal as a function of competitor antibody are shown inFIGS. 12a -12 b. The 12 variant curves shown, those of P257L, P257N,V279E, V279Q, V279Y, {circumflex over ( )}281S, E283F, V284E, L306Y,T307V, V308F, and Q311V, demonstrate increased affinity as each variantcurve is shifted to the left of the wild-type curve in their box.Competition AphaScreen™ data for Fc variants of the present inventionare summarized in FIGS. 13a-13j and 14a -14 d. Additional competitionAlphaScreen™ data in 0.1M sodium phosphate pH 6.0 with 125 mM sodiumchloride are summarized in FIGS. 21a -21 b. The relative FcRn binding ofthe variant compared to wild type are listed. Values greater than onedemonstrate improved binding of the Fc variant to FcRn compared to thewild type. For example, the variant E283L and V284E have 9.5-fold and26-fold stronger binding than the wild type, respectively. Surfaceplasmon resonance measurements of many variants also show increasedbinding to FcRn as shown in FIGS. 15 and 16 a-16 b.

At position 257, all variants that remove the imino acid, proline, andsubstitute an amino acid without the backbone N to side chain covalentbond, allow the backbone more flexibility which allows more freedom forthe Fc domain to better bind FcRn. In particular, variants at position257 to L and N have strong FcRn binding at pH 6, demonstrating that thefour atom side chain and gamma branching pattern of the side chain helpsthe Fc domain make productive, ie strong, FcRn interactions. Position308 interacts with position 257. Both of these positions in turninteract with H310, which is directly involved in the Fc/FcRninteractions (Table 2, Burmeister et al (1994) Nature 372:379-383,entirely incorporated by reference). The Fc variants V308F and V08Y havea 2.9-fold and 4.3-fold increase in FcRn affinity over wild type (FIGS.13a-13j ). Positions 279 and 385 interact with FcRn as variants V279E,V279Q and V279Y and G385H and G385N all have stronger FcRn interactions.These variants all are to amino acids that are capable of hydrogenbonding. Sequences of the Fc regions of human IgG1 comprising variousmodifications of the present invention are shown in FIG. 23.

The Fc variant N434Y has particularly strong binding to FcRn at pH 6.0as shown in FIG. 13a -13 j. The single variant N434Y has 16-foldincreased binding. Combinations of this variant with other modificationsled to even stronger binding. For example, P257L/N434Y, {circumflex over( )}281S/N434Y, and V308F/N434Y show 830-fold, 180-fold, and 350-foldincreases in FcRn binding.

Example 4: Variants Incorporating Insertions and Deletions

Insertions and deletions that alter the strength of Fc/FcRn interactionswere constructed and their binding properties to various Fc ligands weremeasured. An Fc variant with an inserted Ser residue between residues281 and 282, using the EU numbering of Kabat et al, was designed toincrease the FcRn binding properties of the Fc domain. This variant isreferred to as {circumflex over ( )}2815 with “{circumflex over ( )}”meaning an insertion following the position given. AlphaScreen™ datashowing the improved binding of {circumflex over ( )}281S is shown inFIGS. 12b and 21a . The inserted sequence, which may be more than oneresidue, is given after the position number. This Fc variant wasconstructed in the kappa, IgG1 anti-HER2 antibody trastuzumab(Herceptin®, Genetech) using methods disclosed herein. An insertion atthe site between residues 281 and 282 shifts the Fc loop residuesC-terminal of residue 281 toward the C-terminus of the loop and altersthe side chain positioning. Fc variants comprising substitutions atpositions 282, 283, and 284 suggested that the C-terminal shift of thisloop was beneficial (See FIGS. 14a-14d ). Another variant, a deletion ofN286, sometimes referred to as N286#, was also constructed to shift theposition of this FcRn-binding loop. This variant shows increased bindingto FcRn at pH6.0 (FIG. 14b ).

The AlphaScreen™ data shows the binding of the {circumflex over ( )}281Svariant and other variants to FcRn. This AlphaScreen™ data was collectedas a direct binding assay. Higher levels of chemiluminescent signalsdemonstrate stronger binding. As the concentrations of the variants areraised in the assay, stronger signals are created. These data at pH 6.0,in FIGS. 17a and 17b , demonstrate the increased affinity of {circumflexover ( )}281S, P257L, P257L/{circumflex over ( )}281S (a combinationsubstitution/insertion variant) and other variants over the wild-typeFc. Also shown is a double substitution, T250Q/M428L, shown previouslyto have an increased serum half in monkeys (Hinton et al., 2004, J.Biol. Chem. 279(8): 6213-6216, entirely incorporated by reference). Theinsertion, {circumflex over ( )}281S, alone increases the Fc/FcRnbinding. Additionally, {circumflex over ( )}281S further increases thebinding of P257L when the two modifications are combined in the variantP257L/{circumflex over ( )}281S as shown in the ˜40 nM data points. Thedata in FIG. 17c demonstrate that these variants do not show increasedFcRn binding at pH 7.0. The reduced affinity at pH 7.0 is desired forincreased half-life in vivo, because it allows the release of Fcpolypeptides from FcRn into the extracellular space, an important stepin Fc recycling.

Surface plasmon resonance experiments also demonstrate the improvedbinding of {circumflex over ( )}281S to FcRn. FIG. 18 shows the responseunits created as various Fc variant binding to FcRn on the chip surface.After allowing the variant to fully bind to the chip, the response unitsare recorded and shown on the ordinate. The insertion, {circumflex over( )}281S shows binding properties comparable to other variants shownherein to have increased affinity for FcRn over the wild type (See FIGS.13a -13 j, 14 a-14 d and 15, for examples).

The deletion variant comprising a deletion of N286, N286#, also showsincreased affinity for FcRn over wild type. This variant has a 2.0-foldincrease in FcRn affinity as shown in FIG. 13a -13 j. The data thereinare also AlphaScreen™ data collected as a competition experiment at pH6.0. The variants are used to inhibit the binding of wild-type Fc,linked to the donor bead, with FcRn, linked to the acceptor beads.Two-fold less free N286# was needed than free wild-type Fc to inhibitthe binding of the donor/acceptor beads through the Fc/FcRn complex.This demonstrates the 2-fold tighter binding of N286# over the wildtype.

Other Fc variants comprising insertions or deletions have decreasedaffinity for FcRn. The insertion variant, {circumflex over ( )}254N hasgreatly decreased FcRn binding as would be expected from the nature andpositioning of the variant. This variant places the insertion, an Asn,in the middle of an FcRn binding loop. This insertion has only 1.1% ofthe binding of the binding affinity of the wild type (FIGS. 13a-13j ).

Example 5: Combination Variants with Altered FcRn and FcgammaRCharacteristics

As shown in FIG. 13b for the anti-HER2 antibody, the Fc variant P257Lhas increased affinity for FcRn relative to VVT. P257L gave a median of2.6-fold increase in FcRn affinity for human FcRn, pH 6.0 in phosphatebuffer with 25 mM NaCl added. The addition of 1332E or S239D/I332E tothe P257L variant yielded double and triple variants, P257L/I332E andS239D/P257L/I332E, which retain the increased affinity for FcRn. Thevariant S239D/I332E has essentially un-altered FcRn binding compared towild type as shown in the AlphaScreen™ assays in FIG. 14b . These doubleand triple variants had a 5- and 4-fold increased affinity. The I332Eand S239D/I332E variants have improved binding to FcgammaR, inparticular to FcgammaRIIIa (See U.S. Ser. No. 11/124,620, entirelyincorporated by reference). The FcgammaR-binding properties of somevariants of the present invention are shown in FIG. 25. The protein Abinding properties of some variant of the present invention are shown inFIG. 26. Protein A binding is frequently used during purification ofFc-containing proteins. The substitution V308F also improves FcRnbinding at pH 6.0 (FIG. 13e ). V308F has 3-fold increased affinity as asingle substitution in the anti-HER2 antibody trastuzumab (Herceptin™,Genentech) and also has increased affinity when combined withsubstitutions that increase FcgammaR binding, such as I332E,S239D/I332E, and S298A/E333A/K334A (Lazar et al. 2006 Proc. Nat. Acad.Sci USA. 103(111):4005-4010, Shields et al. 2001 J. Biol. Chem.276:6591-6604, both entirely incorporated by reference.) The increasedFcRn binding of G385H is also maintained when combined with FcgammaRimproving substitutions, especially in the triple-substitution variantS239D/I332E/G385H.

Variants with increased binding to FcRn may be combined with variantsthat reduce or knock-out binding to FcgammaR and the complement protein,C1q. The improved binding to FcRn increases the effect from a protectingreceptor allowing for improved half-life. Fc containing proteins mayalso be taken into cells and metabolized through their interaction withthe FcgammaR and the C1q protein. If the Fc/FcgammaR and Fc/C1q proteininteractions are not required for antibody efficacy, deletions of theseinteractions may be made. Deletions of these interactions may alsodecrease the effect of a degrading receptor, thereby also allowing forimproved half-life. In particular the variants 234G, 235G, 236R, 237K,267R, 269R, 325A, 325L, and 328R (U.S. Ser. No. 11/396,495 entirelyincorporated by reference) may be combined with FcRn-improving variantsto create variants with increased FcRn affinity and decreased FcgammaRor C1q affinity. These variants include 235G/257C, 325A/385H, 325A/257L,234G/308F, 234G/434Y, and 269R/308F/311V. These variants may be made inFc domains from IgG1, although reduced interactions with the FcgammaR orC1q may also be achieved by placing these mutations into proteinscomprising Fc domains from IgG2, IgG4, or IgG3. Putting FcRnmodifications, such as 257N, 257L, 257M, 308F, 311V into IgG2 allows fora reduction in FcgammaR binding and increased FcRn interactions.

Variants with decreased binding to FcRn may be combined with variantsthat have increased FcgammaR or C1q binding. The decreased FcRn bindingcombined with increased FcgammaR binding may be beneficial forincreasing the amount of the Fc-containing protein available to illiciteffector functions. Reducing FcRn binding may reduce the amount of theFc-containing protein that is sequestered by FcRn and thus affectbioavailability. Modifications such as I253V, S254N, S254# (deletion of254), T255H, and H435N reduce Fc/FcRn binding (FIG. 13a-13j ) and may becombined with variants with improved FcgammaR binding such as S239D,I332E, H268E, G236A. The resulting Fc domains, such as those comprisingI253V/S239D/I332E, I332E/H435N, or S254N/H268E, have reduced FcRnbinding and increased FcgammaR binding.

Variants with decreased binding to FcRn may be combined with variantswith decreased FcgammaR binding. This combination of decreased FcRn andFcgammaR binding is beneficial in applications such as imaging whereinthe Fc-containing protein is labeled with a radioactive or toxic tracer.Ideally the half-life of the protein comprising the radioactive traceris similar to the half-life of the radionuclide itself. This allowsclearance of the tracer from the body in the same time as the decay ofthe radionuclide. The reduced FcgammaR interactions also allow optimalavailability of the Fc-containing protein for its target. For example,if the Fc-containing protein is an antibody, then the reduce FcgammaRbinding allow more antibody to be assessable to antigen. Combinations ofFcRn- and FcgammaR-affecting variants, such as 235G/254N, 236R/435N,269R/I253V are good for this application.

Example 6: Fc Variants in Antibody OST577 Binding to Human FcRn

OST577 is an anti-Hepatitis B surface antigen antibody (Ehrlich et al.(1992) Hum. Antibodies Hybridomas 3:2-7, entirely incorporated byreference). Heavy and light chain sequences were taken from the KabatDatabase with KADBID 000653 (heavy) and KADBID 007557(light) (Martin AC,Proteins. 1996 May; 25(1):130-3, entirely incorporated by reference).DNA encoding the heavy and light chains were synthesized by Blue HeronBiolotechnology, Bothell, Wash. Wild-type and variant OST577 antibodieswere expressed and purified as in the anti-HER2 (trastuzumab) variantsin EXAMPLE 1. Biacore™ binding assays were performed as in EXAMPLE 2,with a human FcRn/Glutathione D transferase (GST) fusion proteinattached to the chip surface. As shown in FIG. 19, Fc variants of thepresent invention have altered binding to human FcRn. Variants withincreased binding adhere more easily to the FcRn on the surface andcause a greater rise in Response Units (RU's). The variants shown withmodification in the FcRn-binding region all have increased affinity forFcRn compared to the wild-type protein. These variants include P257L,P257N, V308F, N434Y, P257L/N434Y and P257L/V308F. The variant with the3^(rd) most RU's at 975 seconds, T250Q/M428L, has been shown to increasethe half life of OST577 antibodies in macaques (Hinton et al. 2004Journal of Biological Chemistry 279(8):6213-6216, Hinton et al. 2006Jounal of Immunology 176:346-356, both entirely incorporated byreference). Included in this data set is an antibody with a hybridIgG1/IgG2 heavy chain constant region containing the substitutionsS239D/I332E. As described in EXAMPLE 5, these substitutions increase theantibody affinity for FcgammaR. As shown in FIG. 19, these substitutionsdo not alter the FcRn-binding properties, as the hybrid S239D/I332EBiacore™ traces overlay the wild-type traces containing kappa or lambdaCL1 domains.

Example 7: Affinity of Fc Variants for Human, Monkey and Mouse FcRn

Fc variants in the anti-HER2 antibody trastuzumab were created asdescribed in EXAMPLE 1. Surface plasmon resonance (SPR) traces werecollected as described in EXAMPLE 2, except that human, macaque or mouseFcRn was attached to the chip surface. Two SPR curves were collected foreach Fc variant with differing amounts of GST-FcRn attached to thesurface. Each curve was fit to a 1:1 Langmuir binding model and the tworesulting Kd values were averaged to produce a representative value foreach variant-receptor pair. The results are presented in FIG. 20 as thefold-improvement in Kd compared to the wild-type trastuzumab. Forexample, the variant V308F/Q311V has 3.4-fold tigher binding to humanFcRn than does the wild type. V308F/Q311V also has 3.7-fold and 5.1-foldtigher binding to monkey and mouse FcRn, respectively. The variant M428Lhas been shown to increase the antibody half-life (Hinton et al. 2004Journal of Biological Chemistry 279(8):6213-6216, entirely incorporatedby reference) and has a 2.4-, 2.0, and 2.1-fold increased binding to thehuman, monkey and mouse FcRn's, respectively. Other variants, includingP257L, P257N, N434Y, Q311V, V308F, V308F/N434Y, P257L/V308F, andP257L/N434Y, also show increased binding at pH6.0.

Example 8: FcRn Variants in Various Fc Domains

Variants of the present invention may be incorporated into any constantdomain, using the molecular biology and purification techniquesdescribed herein, including those in EXAMPLE 1. Amino acid sequences ofthe IgG1, IgG2, IgG3, and IgG4 constant domains may be used as listed inFIG. 2. In addition, combinations of two or more different constantdomains may be used. For example, FIG. 24 lists some of themodifications found in the present invention incorporated into a hybridof IgG1 and IgG2. This hybrid comprises the IgG2 CH1 domain and the IgG1CH2 and CH3 domains. IgG3 has a lower half-life in humans compared toIgG1, IgG2, and IgG4 (7 days vs ˜21 days, Janeway, Travers, Walport,Shlomchik. Immunology, 5^(th) ed. Garland Publishing c2001, FIG. 4-16,incorporated by reference) and is therefore desirable in certainapplications.

Example 9: Creation of Variant in an Anti-VEGF Antibody

Anti-VEGF antibodies with altered binding were produced using themethods described herein, including EXAMPLE 1. The wild type anti-VEGFheavy chain comprises the following sequence of amino acids:

EVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTCPPCPAPELLGGPSVFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNVVYVDGVEVHNAKTKPREEQYNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLPPSREEMTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKLTVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK

The wild-type anti-VEGF light chain comprises the following sequence ofamino acids:

DIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKIDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Single and combination variants with altered binding include thevariants shown in FIG. 28, which shows the variants produced, the volumeof culture media used, and the resulting yield of the antibody variants.Numbering for the variants follows the EU index as in Kabat et al. Thevariants listed in FIG. 28 were produced in either IgG1 or hybrid VHcomprising sequences from both IgG1 and IgG2. These variants contain thevariable region that binds the antigen VEGF. All proteins were judged tobe >90% pure by size exclusion chromatography and SDS gelelectrophoresis.

Example 10: In Vivo Half-Life of Antibody Variants

The pharmacokinetics of wild-type and variant antibodies were studied inmice. The mice used were defiecient in the expression of mouse FcRn(B6-Fcgt^(Tm1Dcr) mice) and were heterozygous for the knock-in of humanFcRn (hFcRn Tg—transgene) as described in Petkova et al. InternationalImmunology 2006 December; 18(12):1759-69. Petkova et al showed that thevariant N434A has an increased half-life in these human FcRn knock-inmice, which agrees with earilier results showing that the N434A varianthas increased half life in monkeys (U.S. application Ser. No.11/208,422, publication number US26067930A1). Female mice aged 9-12weeks were injected intravenously with 2 mg/kg antibody in groups of 6mice per antibody. Blood samples were collected at 1 hr, and days 1, 4,8, 11, 15, 18, 21, 25 and 28 from the oribital flexus. The concentrationof each antiobody in serum was measured with a sandwich ELISA assayusing anti-human Fc antibodies and europium detection.

The results of the study are shown in FIG. 27, which are representativedata of two separate studies. The mean and standard deviation of themean for the four samples are shown. Clearly, the V308F variant haslonger half-life, remaining at measurable concentrations out to 25 days.The VVT and P257L and P257N variants are cleared more quickly, onlyhaving measurable concentrations out to 15, 8, and 4 days, respectively.The serum concentrations as a function of time were fit to anon-compartimental model using the software package, WinNonLin(Pharsight Inc). The terminal half-life of the V308F variant was 4.9days, whereas the terminal half-lives of the VVT and P257L and P257Nvariants were 3.0, 1.9 and 0.9 days, respectively. The area under thecurves (AUC) of the V308F variant was 129 day*ug/ml, whereas those ofthe VVT and P257L and P257N variants were 70, 38 and 38 day*ug/ml,respectively.

Example 11: FcRn Binding Experiments at pH 6.0

Anti-VEGF variants of the present invention were tested for theirbinding ability to human FcRn with Biacore assays as described inEXAMPLE 2 with some modifications. Human FcRn was attached covalently toa CM5 chip in 10 mM sodium acetate, pH 4.5 on usingN-hydroxysuccinimide/N-ethyl-N′-(-3-dimethylamino-propyl) carbodiimide(NHS/EDC) at a flow rate of 5 ul/min. The human FcRn used contained GSTand HIS tagged version to aid in purification and other assys.Approximately 3300 RU of FcRn was attached to the chip. Flow cell 1 wasmocked with NHS/EDC as a negative control of binding. Running buffer was25 mM phosphate buffer pH6.0, 150 mM NaCl, 3 mM EDTA and 0.005% (v/v)Surfactant P20. Antibodies were washed off the FcRn chip with the samebuffer at pH7.4, which quickly removed all variants tested. The biacoreassociation and dissociation traces were fit to a conformationalexchange model to calculate an apparent equilibrium binding constant,Kd.

The results demonstrate that the V308F variant and many other variantshave improved binding to FcRn. The wild-type anti-VEGF antibody had a Kdof 18 nM, which differs considerably from the value reported in Dall'Acqua et al (Dall' Acqua et al Journal of Immunology 2002,169:5171-5180) because of the differences in assay design and datafitting. Our assay format gave reproducible results if the FcRn chip wasused soon after creation. The FcRn chip, however, degraded with use,possibly from the dissociation of either the two FcRn chains from thesurface. The results demonstrate the altered binding of the variantscompared to wild-type anti-VEGF. FIG. 29 shows the fold increase inbinding strength relative to the wild-type control. Values greater thanone show that the variant antibody has has higher affinity for FcRn thanthe wild-type protein. The variant V308F, for example, binds FcRn 4.5fold more tightly than the wild-type antibody. The variant V308F/M428Lbinds FcRn 12.3 fold more tightly and the variant T307P/V308F binds FcRn3.16 fold more tightly than the wild-type protein. No variants shown inFIG. 29 have reduced affinity for FcRn compared to the wild-type (valueswould be less than 1.0). The variant N434S has an FcRn binding affinity4.4 fold stronger than VVT, comparable to V308F.

Example 12: Binding Experiments to Transmembrane FcRn

FcRn alpha chain and beta-2-microglobulin cDNA was ordered from OriGeneTechnologies Inc (Rockville, Md.) and transfected in 293T cells toexpress functional FcRn on the cell surface. 20 ug Fcgrt and 40 ug ofbeta-2-microglobulin DNA was transfected with lipofectamine (InvitrogenInc.) and the cells were allowed to grow for 3 days in DMEM media with10% ultra low IgG serum. Control cells not transfected with the two FcRnchains were also grown. Varying amounts of anti-VEGF antibodies (WT andvariants) were bound to the cells for 30 minutes in 25 mM phosphatebuffer pH6.0, 150 mM NaCl, 0.5% BSA and then washed 6-9 times in 25 mMphosphate buffer pH6.0, 150 mM NaCl, 0.5% BSA plus 0.003% igepal. Afterwashing, antibodies were fixed to the surface by treatment with thebinding with 1% PFA. Bound antibodies were than detected using a PEtagged Fab′₂ against human Fab domains and the mean fluorescenceintensity (MFI) was measured using a BD FACS Canto II. The average oftwo samples per antibody are presented in FIG. 30. The curve fits to thedata in FIG. 30 do not provide interpretable EC50 values because manycurves did not form an upper baseline by saturating the cells. Theantibodies may be ranked in order of their binding affinity, however, byreporting the log[variant] at which the MFI equals 3000, EC(MFI=3000).Using this metric, the antibodies may be listed from strongest toweakest FcRn affinity as follows: V308F/M428L, V2591/V308F, T2501/V308F,T250Q/M428L, N434S, T307Q/V308F, P257L, T307S/V308F, V308F, T256VN308F,V308F/L309Y, and WT.

Example 13: Characteristics of the Variant, 434S

Antibodies comprising the modification 434S have particularly favorableproperties making them preferred variants of the present invention. Inhuman IgG1, the wild-type residue is an asparagine, Asn, at position 434so that this variant may be referred to as N434S in the context of IgG1or other Fc domains which contain Asn, N, at position 434. Moregenerally, this variant may be referred to simply as 434S. Herein, the434S variant has been produced successfully in both the anti-HER2antibody trastuzumab and the anti-VEGF antibody.

The Ser at position 434 has the ability to hydrogen bond with FcRneither directly or indirectly, ie, mediated by water or solutemolecules. The gamma oxygen of Ser at position 434 is in the vicinity ofthe carbonyl oxygen atoms of Gly131 and Pro134 on the FcRn molecule, asshown in FIG. 32. FIG. 32 shows a model of the human Fc domain incomplex with human FcRn. The Fc domain in the model comprises the 434Ssubstitution, hence residue 434 is Ser in FIG. 32. The model is createdwith PDA® technologies (Dahiyat and Mayo Protein Sci. 1996 May;5(5):895-903), the crystal structure of the rat Fc domain bound to therat FcRn (Martin et al. Mol Cell. 2001 April; 7(4):867-77), and Pymol(Delano Scientific). The small size of Ser is easily accomidated in theinterface between the two proteins.

The antibody variant N434S has a 4.4-fold increased binding affinity forFcRn compared to the wild-type antibody as shown by biacore™measurements (FIG. 29). The variant also shows increased binding to cellsurface bound FcRn as shown by cell counting measurements (FIG. 30).

Based on the results shown in FIGS. 29 and 30, preferred variantscomprising 434S and other modifications are expected to includeV308F/434S, 428L/434S, 252Y/434S, 259I/308F/434S, 250I/308F/434S, and307Q/308F/434S.

Example 14: Additional Variants

Additional variants may be based on the data contained herein and in theliterature (Dall' Acqua et al Journal of Biological Chemistry 2006 Aug.18; 281(33):23514-24; Petkova et al. International Immunity 2006December; 18(12):1759-69; Dall' Acqua et al Journal of Immunology 2002,169:5171-5180; Hinton et al, Journal of Biological Chemistry 2004279(8): 6213-6216; Shields et al. Journal of Biological Chemistry 2001276(9):6591-6604; Hinton et al. Journal of Immunology 2006, 176:346-356,all incorporated by reference). These variants include those found inFIGS. 31a -31 b.

Based on the results in FIGS. 29 and 30 and the results of Dall' Acquaet al (Journal of Biological Chemistry 2006 Aug. 18; 281(33):23514-24,incorporated by reference), preferred variants include Y319L, T307Q,V259I, M252Y, V259I/N434S, M428L/N434S, V308F/N434S,M252Y/S254T/T256E/N434S, M252Y/S254T/T256E/V308F,M252Y/S254T/T256E/M428L, V308F/M428L/N434S, V2591/V308F/N434S,T307Q/V308F/N434S, T250I/V308F/N434S, V308F/Y319L/N434S,V259I/V308F/M428L, V259I/T307Q/V308F, T250I/V259I/V308F,V259I/V308F/Y319L, T307Q/V308F/L309Y, T307Q/V308F/Y319L, andT250Q/V308F/M428L.

Based on the results in FIGS. 29 and 30 more preferred variants includeY319L, T307Q, V259I, M252Y, V259I/N434S, M428L/N434S, V308F/N434S,V308F/M428L/N434S, V259I/V308F/N434S, T307Q/V308F/N434S,T250I/V308F/N434S, V308F/Y319L/N434S, V259I/V308F/M428L,V259I/T307Q/V308F, T250I/V259I/V308F, V259I/V308F/Y319L,T307Q/V308F/L309Y, T307Q/V308F/Y319L, and T250Q/V308F/M428L.

Whereas particular embodiments of the invention have been describedabove for purposes of illustration, it will be appreciated by thoseskilled in the art that numerous variations of the details may be madewithout departing from the invention as described in the appendedclaims. All references cited herein are incorporated in their entirety.

1.-24. (canceled)
 25. A protein comprising an Fc variant as compared toa parent IgG Fc region, said variant Fc region comprising an amino acidsubstitution selected from the group consisting of Q311V, H285D andN286D, wherein numbering is according to the EU index in Kabat et al.26. An antibody comprising an Fc variant as compared to a parent IgG Fcregion, said variant Fc region comprising an amino acid substitutionselected from the group consisting of Q311V, H285D and N286D, whereinnumbering is according to the EU index in Kabat et al.
 27. A nucleicacid encoding the protein of claim
 25. 28. A nucleic acid encoding theheavy chain of said antibody of claim
 26. 29. An expression vectorcomprising the nucleic acid of claim
 27. 30. A host cell comprising theexpression vector of claim
 29. 31. A method of making a proteincomprising an Fc variant as compared to a parent IgG Fc region, saidvariant Fc region comprising an amino acid substitution selected fromthe group consisting of Q311V, H285D and N286D, wherein numbering isaccording to the EU index in Kabat et al., said method comprisingculturing the host cell of claim 30 under conditions wherein saidantibody is expressed and recovering said antibody.